date:20191103

Re: [ccp4bb] Unusual dataset with high Rmerge and extremely low b-factors?

2019-11-03 Thread Anastassis Perrakis

Dear Michael,

Exactly because the B factor is only 8, the intensity as function of resolution 
is droping really slowly, and thus the I/sigI 4.7 at low resolution drops so 
slowly to 1.0.

I would almost bet you have a low solvent content.

The data are fine imo.

Best,

Tassos

On Nov 4, 2019, at 0:18, Michael Jarva 
mailto:jarv...@wehi.edu.au>> wrote:

Hi CCP4BB,

I have some unusual crystal diffraction data I'd like to get your input on.

Almost a year ago I shot some small rods sticking out of a loop, so basically 
no liquid around them - using the microfocus MX2 beamline at the australian 
synchrotron, collected on an EIGER 16M detector.

The crystals diffracted weakly and was seemingly not viable at first glance 
because of high Rmerge/Rpims. See the aimless summary at the bottom of this 
post. This seemed to stem from a low spot intensity at low resolutions 
(I/sd(I)=4.6), but since the CC1/2 was fine I went with it anyway.

Here I also noted an unusually low Mosaicity, 0.05, and Wilson B-factors, 8.02 
Å^2.

Density maps looked great and the build refined easily enough (R/Rfree 
0.1939/0.2259) with a mean B-factor of 19.85, which according to phenix is 
lower than any other structure deposited in that resolution bin. Furthermore, 
the molprobity score is 0.83, and overall real-space correlation CC is 0.855.

So my question is, can I feel comfortable depositing this?

best regards
Michael

Chosen Solution:space group P 1 21 1
Unit cell:44.93   41.90   45.83  90.00  115.57   90.00
Number of batches in file:   1659
The data do not appear to be twinned, from the L-test
Overall InnerShell OuterShell

Low resolution limit   41.34 41.34  2.49

High resolution limit   2.40  8.98  2.40


Rmerge  (within I+/I-) 0.231 0.084 0.782

Rmerge  (all I+ and I-)0.266 0.099 0.983

Rmeas (within I+/I-)   0.323 0.118 1.091

Rmeas (all I+ & I-)0.317 0.118 1.167

Rpim (within I+/I-)0.225 0.084 0.759

Rpim (all I+ & I-) 0.171 0.063 0.623

Rmerge in top intensity bin0.079- -

Total number of observations   19901   362  2067

Total number unique 6054   126   611

Mean((I)/sd(I))  2.7   4.6   1.0

Mn(I) half-set correlation CC(1/2) 0.958 0.991 0.570

Completeness98.6  98.2  97.3

Multiplicity 3.3   2.9   3.4

Mean(Chi^2) 0.48  0.33  0.50


Anomalous completeness  81.7  92.2  75.1

Anomalous multiplicity   1.5   1.8   1.9

DelAnom correlation between half-sets -0.003 0.041 0.045

Mid-Slope of Anom Normal Probability   0.704   - -


The anomalous signal appears to be weak so anomalous flag was left OFF


Estimates of resolution limits: overall

   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
resolution

   from Mn(I/sd) >  1.50: limit =  2.67A

   from Mn(I/sd) >  2.00: limit =  2.87A


Estimates of resolution limits in reciprocal lattice directions:

  Along0.96 a* - 0.28 c*

   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
resolution

   from Mn(I/sd) >  1.50: limit =  2.40A  == maximum 
resolution

  Along k axis

   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
resolution

   from Mn(I/sd) >  1.50: limit =  2.86A

  Along   -0.17 a* + 0.99 c*

   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
resolution

   from Mn(I/sd) >  1.50: limit =  2.98A


Anisotropic deltaB (i.e. range of principal components), A^2:  8.62


Average unit cell:44.93   41.90   45.83   90.00  115.57   90.00

Space group: P 1 21 1

Average mosaicity:   0.05


Minimum and maximum SD correction factors: Fulls   1.27   1.28 Partials   0.00  
 0.00





Michael Jarva, PhD
ACRF Chemical Biology Division
The Walter and Eliza Hall Institute of Medical Research
1G Royal Parade
Parkville Victoria 3052
Australia
Phone: +61 3 9345 2493
Email: jarv...@wehi.edu.au | Web: 
http://www.wehi.edu.au/
The ACRF Chemical Biology Division is supported by the
Australian Cancer Research Foundation


___

The information in this email is confidential and intended solely for the 
addressee.
You must not disclose, forward, print or use it without the permission of the 
sender.

The Walter and Eliza Hall Institute acknowledges the Wurundjeri people of the 
Kulin
Nation as the traditional

[ccp4bb] Phenix version 1.17 released

2019-11-03 Thread Paul Adams

The Phenix developers are pleased to announce that version 1.17 of Phenix is 
now available (build 1.17.1-3660). Binary installers for Linux, Mac OSX, and 
Windows platforms, and the source installer, are available at the download site:

http://phenix-online.org/download/

Please note that there is a new publication that describes recent Phenix 
developments for structure determination with X-rays, neutrons and electrons:

https://doi.org/10.1107/S2059798319011471

Highlights for the 1.17 version of Phenix:

1.17.1 Changes

- Fix bug on Windows where xtriage results would fail to display
- Other bug fixes

1.17 Changes

- Improved handling of SHELX data in phenix.reflection_file_converter
- eLBOW can output files for Amber and supports the Orca QM package
- dials.image_viewer is used for viewing diffraction images
- Updated map smoothing
- Fix inconsistency in clashscore values in phenix.validation_cryoem when 
hydrogens are in the model

For a full list of changes see:

http://www.phenix-online.org/documentation/CHANGES

Please note that this new publication should be used to cite the use of Phenix:

Macromolecular structure determination using X-rays, neutrons and electrons: 
recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, 
Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner 
RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, 
Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams 
CJ, Adams PD: Acta Cryst. (2019). D75, 861-877.

Full documentation is available here:

http://www.phenix-online.org/documentation/

There is a Phenix bulletin board:

http://www.phenix-online.org/mailman/listinfo/phenixbb/

Please consult the installer README file or online documentation for 
installation instructions.

Direct questions and problem reports to the bulletin board or:

h...@phenix-online.org and b...@phenix-online.org

Commercial users interested in obtaining access to Phenix should visit the
Phenix website for information about the Phenix Industrial Consortium.

The development of Phenix is principally funded by the National Institute of
General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge
the generous support of the members of the Phenix Industrial Consortium.

-- 
Paul Adams
Division Director, Molecular Biophysics & Integrated Bioimaging, Berkeley Lab 
(http://biosciences.lbl.gov/divisions/mbib)
Principal Investigator, Computational Crystallography Initiative, Berkeley Lab 
(http://cci.lbl.gov)
Vice President for Technology, the Joint BioEnergy Institute 
(http://www.jbei.org)
Principal Investigator, ALS-ENABLE, Advanced Light Source, Berkeley Lab 
(http://als-enable.lbl.gov)
Division Deputy for Biosciences, Advanced Light Source, Berkeley Lab 
(https://als.lbl.gov)
Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov)
Adjunct Professor, Department of Bioengineering, U.C. Berkeley 
(http://bioeng.berkeley.edu)
Adjunct Professor, Comparative Biochemistry, U.C. Berkeley 
(http://compbiochem.berkeley.edu)

Building 33, Room 347
Building 978, Room 4126
Building 977, Room 180C
Tel: 1-510-486-4225
http://cci.lbl.gov/paul

Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 33R0345
Berkeley, CA 94720, USA.

Executive Assistant: Nikki Humphreys [ nhumphr...@lbl.gov ][ 1-510-486-4610 ]
--



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Re: [ccp4bb] Unusual dataset with high Rmerge and extremely low b-factors?

2019-11-03 Thread Jon Cooper

Given that the I/sigma(I) is quite low the high R-merge values are probably to be expected. If the data were stronger, an R-merge that high would indicate that the space group was wrong or the data misindexed. If the multiplicity was higher you could process the data in lower symmetry space group (P1) and see if the R-merge became appreciably lower, but I'm not sure that it will be sensible to do that with such a low multiplicity, still it's probably worth doing. I think if you explain the vagaries of the crystals and data when you publish and/or deposit, I think it should be OK with the referees, especially if the map looks good. I would not worry too much about the mean B-factor but it might be interesting to see the Wilson plot.On 3 Nov 2019 23:18, Michael Jarva  wrote:

Hi CCP4BB,




I have some unusual crystal diffraction data I'd like to get your input on.




Almost a year ago I shot some small rods sticking out of a loop, so basically no liquid around them - using the microfocus MX2 beamline at the australian synchrotron, collected on an EIGER 16M detector.




The crystals diffracted weakly and was seemingly not viable at first glance because of high Rmerge/Rpims. See the aimless summary at the bottom of this post. This seemed to stem from a low spot intensity at low resolutions (I/sd(I)=4.6), but since the CC1/2
 was fine I went with it anyway.




Here I also noted an unusually low Mosaicity, 0.05, and Wilson B-factors, 8.02 Å^2.




Density maps looked great and the build refined easily enough (R/Rfree 0.1939/0.2259) with a mean B-factor of 19.85, which according to phenix is lower than any other structure deposited in that resolution bin. Furthermore, the
 molprobity score is 0.83, and overall real-space correlation CC is 0.855.




So my question is, can I feel comfortable depositing this? 




best regards

Michael





Chosen Solution:    space group P 1 21 1

Unit cell:    44.93   41.90   45.83      90.00  115.57   90.00

Number of batches in file:   1659

The data do not appear to be twinned, from the L-test



Overall InnerShell OuterShell



Low resolution limit   41.34 41.34  2.49
High resolution limit   2.40  8.98  2.40

Rmerge  (within I+/I-) 0.231 0.084 0.782
Rmerge  (all I+ and I-)0.266 0.099 0.983
Rmeas (within I+/I-)   0.323 0.118 1.091
Rmeas (all I+ & I-)0.317 0.118 1.167
Rpim (within I+/I-)0.225 0.084 0.759
Rpim (all I+ & I-) 0.171 0.063 0.623
Rmerge in top intensity bin0.079- - 
Total number of observations   19901   362  2067
Total number unique 6054   126   611
Mean((I)/sd(I))  2.7   4.6   1.0
Mn(I) half-set correlation CC(1/2) 0.958 0.991 0.570
Completeness98.6  98.2  97.3
Multiplicity 3.3   2.9   3.4
Mean(Chi^2) 0.48  0.33  0.50

Anomalous completeness  81.7  92.2  75.1
Anomalous multiplicity   1.5   1.8   1.9
DelAnom correlation between half-sets -0.003 0.041 0.045
Mid-Slope of Anom Normal Probability   0.704   - -  

The anomalous signal appears to be weak so anomalous flag was left OFF

Estimates of resolution limits: overall
   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum resolution
   from Mn(I/sd) >  1.50: limit =  2.67A 
   from Mn(I/sd) >  2.00: limit =  2.87A 

Estimates of resolution limits in reciprocal lattice directions:
  Along0.96 a* - 0.28 c*
   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum resolution
   from Mn(I/sd) >  1.50: limit =  2.40A  == maximum resolution
  Along k axis
   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum resolution
   from Mn(I/sd) >  1.50: limit =  2.86A 
  Along   -0.17 a* + 0.99 c*
   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum resolution
   from Mn(I/sd) >  1.50: limit =  2.98A 

Anisotropic deltaB (i.e. range of principal components), A^2:  8.62

Average unit cell:44.93   41.90   45.83   90.00  115.57   90.00
Space group: P 1 21 1
Average mosaicity:   0.05

Minimum and maximum SD correction factors: Fulls   1.27   1.28 Partials   0.00   0.00















Michael Jarva, PhD
ACRF Chemical Biology Division

The Walter and Eliza Hall Institute of Medical Research
1G Royal Parade
Parkville Victoria 3052
Australia

Phone: +61 3 9345 2493 
Email: jarv...@wehi.edu.au | Web: http://www.wehi.edu.au/

The ACRF Chemical Biology

Re: [ccp4bb] Sodium Ion Binding?

2019-11-03 Thread Artem Evdokimov

Hi Jacob

Not the easiest task... Based on past experience your major issue will be
the incredible abundance of sodium ions in everything.

So assuming you have high quality sodium free solutions and are willing to
work exclusively in plastic, quartz or fused silica - here are a few
thoughts:

1. Na-22 isotope binding. An oldie but goodie.
2. Sodium-reactive dye equilibrium (see e.g. reference I put at the end)
3. Flame or ion coupled plasma spectroscopy. Very nice to do given the
marvellous sodium band.
4. Sodium selective glass electrode (requires more solution of your analyte
than the other methods)

Overall the key component to these methods is your ability to displace the
sodium with something else prior to measuring the effect of titration the
ion back. Isotopic Na is easier in this regard - but at a cost...

Hope this helps.

Artem

https://bmcresnotes.biomedcentral.com/articles/10.1186/1756-0500-6-556

https://www.google.com/url?sa=t=web=j=http://clinchem.aaccjnls.org/content/clinchem/24/4/580.full.pdf=2ahUKEwis5KL_vM_lAhXCmuAKHY2cAVQQFjAFegQIARAB=AOvVaw0Yhz23Yr_ulB85MDQspIFl=1572833723049


On Sun, Nov 3, 2019, 20:41 Keller, Jacob  wrote:

> Dear Crystallographers,
>
>
>
> Does anyone know of a good biophysical way to identify or quantify sodium
> ion binding to a protein, besides crystallography and ITC? Is this possible
> with SPR, perhaps? Mass spec? Gel shifts? Examples would be greatly
> appreciated!
>
>
>
> All the best,
>
>
>
> Jacob Keller
>
>
>
>
>
> +
>
> Jacob Pearson Keller
>
> Research Scientist / Looger Lab
>
> HHMI Janelia Research Campus
>
> 19700 Helix Dr, Ashburn, VA 20147
>
> Desk: (571)209-4000 x3159
>
> Cell: (301)592-7004
>
> +
>
>
>
> The content of this email is confidential and intended for the recipient
> specified in message only. It is strictly forbidden to share any part of
> this message with any third party, without a written consent of the sender.
> If you received this message by mistake, please reply to this message and
> follow with its deletion, so that we can ensure such a mistake does not
> occur in the future.
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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[ccp4bb] Sodium Ion Binding?

2019-11-03 Thread Keller, Jacob

Dear Crystallographers,

Does anyone know of a good biophysical way to identify or quantify sodium ion 
binding to a protein, besides crystallography and ITC? Is this possible with 
SPR, perhaps? Mass spec? Gel shifts? Examples would be greatly appreciated!

All the best,

Jacob Keller


+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.




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[ccp4bb] Unusual dataset with high Rmerge and extremely low b-factors?

2019-11-03 Thread Michael Jarva

Hi CCP4BB,

I have some unusual crystal diffraction data I'd like to get your input on.

Almost a year ago I shot some small rods sticking out of a loop, so basically 
no liquid around them - using the microfocus MX2 beamline at the australian 
synchrotron, collected on an EIGER 16M detector.

The crystals diffracted weakly and was seemingly not viable at first glance 
because of high Rmerge/Rpims. See the aimless summary at the bottom of this 
post. This seemed to stem from a low spot intensity at low resolutions 
(I/sd(I)=4.6), but since the CC1/2 was fine I went with it anyway.

Here I also noted an unusually low Mosaicity, 0.05, and Wilson B-factors, 8.02 
Å^2.

Density maps looked great and the build refined easily enough (R/Rfree 
0.1939/0.2259) with a mean B-factor of 19.85, which according to phenix is 
lower than any other structure deposited in that resolution bin. Furthermore, 
the molprobity score is 0.83, and overall real-space correlation CC is 0.855.

So my question is, can I feel comfortable depositing this?

best regards
Michael

Chosen Solution:space group P 1 21 1
Unit cell:44.93   41.90   45.83  90.00  115.57   90.00
Number of batches in file:   1659
The data do not appear to be twinned, from the L-test
Overall InnerShell OuterShell

Low resolution limit   41.34 41.34  2.49

High resolution limit   2.40  8.98  2.40


Rmerge  (within I+/I-) 0.231 0.084 0.782

Rmerge  (all I+ and I-)0.266 0.099 0.983

Rmeas (within I+/I-)   0.323 0.118 1.091

Rmeas (all I+ & I-)0.317 0.118 1.167

Rpim (within I+/I-)0.225 0.084 0.759

Rpim (all I+ & I-) 0.171 0.063 0.623

Rmerge in top intensity bin0.079- -

Total number of observations   19901   362  2067

Total number unique 6054   126   611

Mean((I)/sd(I))  2.7   4.6   1.0

Mn(I) half-set correlation CC(1/2) 0.958 0.991 0.570

Completeness98.6  98.2  97.3

Multiplicity 3.3   2.9   3.4

Mean(Chi^2) 0.48  0.33  0.50


Anomalous completeness  81.7  92.2  75.1

Anomalous multiplicity   1.5   1.8   1.9

DelAnom correlation between half-sets -0.003 0.041 0.045

Mid-Slope of Anom Normal Probability   0.704   - -


The anomalous signal appears to be weak so anomalous flag was left OFF


Estimates of resolution limits: overall

   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
resolution

   from Mn(I/sd) >  1.50: limit =  2.67A

   from Mn(I/sd) >  2.00: limit =  2.87A


Estimates of resolution limits in reciprocal lattice directions:

  Along0.96 a* - 0.28 c*

   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
resolution

   from Mn(I/sd) >  1.50: limit =  2.40A  == maximum 
resolution

  Along k axis

   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
resolution

   from Mn(I/sd) >  1.50: limit =  2.86A

  Along   -0.17 a* + 0.99 c*

   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
resolution

   from Mn(I/sd) >  1.50: limit =  2.98A


Anisotropic deltaB (i.e. range of principal components), A^2:  8.62


Average unit cell:44.93   41.90   45.83   90.00  115.57   90.00

Space group: P 1 21 1

Average mosaicity:   0.05


Minimum and maximum SD correction factors: Fulls   1.27   1.28 Partials   0.00  
 0.00





Michael Jarva, PhD
ACRF Chemical Biology Division

The Walter and Eliza Hall Institute of Medical Research
1G Royal Parade
Parkville Victoria 3052
Australia

Phone: +61 3 9345 2493
Email: jarv...@wehi.edu.au | Web: http://www.wehi.edu.au/

The ACRF Chemical Biology Division is supported by the

Australian Cancer Research Foundation


___

The information in this email is confidential and intended solely for the 
addressee.
You must not disclose, forward, print or use it without the permission of the 
sender.

The Walter and Eliza Hall Institute acknowledges the Wurundjeri people of the 
Kulin
Nation as the traditional owners of the land where our campuses are located and
the continuing connection to country and community.
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[ccp4bb] ISCSM2020

2019-11-03 Thread Amit Naglekar

Dear All,

On behalf of the organizing committee, we would like to invite you and your
group members to participate at the International Symposium on Cell Surface
Macromolecules to be held in IISER and NCL Pune, India from Feb 17-20, 2020.

This meeting is part of a series held once in 3 years to bring together
people working on diverse aspects of membrane biology. A unique feature of
this meeting is the intense discussion and scope for collaboration. This
will be its 12th edition and will be co-organized by young members of the
Indian scientific community.

See link below for details.

https://www.iscsm2020pune.com/


Regards
AMIT NAGLEKAR
Junior Research Fellow
CSIR-National Chemical Laboratory, Pune, India



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Re: [ccp4bb] Unusual dataset with high Rmerge and extremely low b-factors?

[ccp4bb] Phenix version 1.17 released

Re: [ccp4bb] Unusual dataset with high Rmerge and extremely low b-factors?

Re: [ccp4bb] Sodium Ion Binding?

[ccp4bb] Sodium Ion Binding?

[ccp4bb] Unusual dataset with high Rmerge and extremely low b-factors?

[ccp4bb] ISCSM2020

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