Re: [ccp4bb] detergent crystals

2009-08-04 Thread Pascal Egea 
Hi Jose,
It is quite difficult to crystallize DDM. The main problem is to estimate
detergent concentration in the final sample.
One method requires the use of chromatographic workstation coupled to a
light scattering detector and refraction index measurement unit. In this
case you can know if there is an excess detergent (particularly likely to be
the case if you are using a low CMC detergent like DDM and if you have been
concentrating your sample on a membrane with a cutoff smaller than the empty
micelles). This is more involved and requires a specialized equipment. But
you can detect both your protein and your excess detergent (if there is).
Also to test you crystals, you may want to see if you can access a
fluorescence microscope. If your protein contains tryptophan (and you have
the correct wavelength) then you protein crystals should glow. Your
detergent crystals should not. Those microscopes are getting more and more
popular so maybe you have one next by. It is very convenient.

Hope this helps

Pascal Egea, PhD
University of California Los Angeles
Department of Biological Chemistry

Re: [ccp4bb] resolution shells for each bin in scala?

2009-08-04 Thread Francis E Reyes 

I was hoping for a break down for each bin similar to that of d*trek..


for example:

Rmerge vs Resolution

 Resolution   AverageNum Num   I/sig  I/sig  Rducd  Model  
Rmerge Rmerge
range  counts   rejs   mults   unavgavg  ChiSq  Eadd*   
shell  cumul


 45.96 - 5.45 810211159710.5   19.9   0.85   0.06   
0.043  0.043
  5.45 - 4.33 565 401640 6.9   12.6   0.84   0.10   
0.074  0.056
  4.33 - 3.78 387 341633 4.68.5   0.91   0.15   
0.114  0.069
  3.78 - 3.43 245 371679 3.36.1   0.93   0.22   
0.172  0.081
  3.43 - 3.19 166 381676 2.74.8   1.04   0.28   
0.239  0.093
  3.19 - 3.00 126 311675 2.34.1   1.05   0.34   
0.288  0.104
  3.00 - 2.85 110 131664 2.13.6   1.11   0.39   
0.325  0.114
  2.85 - 2.73 101  31259 2.03.0   1.03   0.42   
0.313  0.119
  2.73 - 2.62  99  2 870 2.02.7   1.02   0.41   
0.308  0.121
  2.62 - 2.53  97  0 512 1.92.4   0.84   0.42   
0.287  0.122


 45.96 - 2.53 304409   14205 4.27.6   0.96   0.16   
0.122  0.122



The last resolution bin has a slice of 2.62 and 2.53 data. I would  
like those for every resolution listed.


FR

On Aug 4, 2009, at 3:25 AM, Phil Evans wrote:

The table has 1/d^2 and Dmin for the outer edge of each bin (columns  
2  3)


Phil

By  4SINTH/LASQ bins (all statistics relative to Mn(I))
__

applet width= 700 height= 300 code=JLogGraph.class
codebase=/usr/local/CCP4versions/Clapham/ccp4-6.1.1/binparam  
name=table value=

$TABLE: Analysis against resolution , New :
$GRAPHS: I/sigma, Mean Mn(I)/sd(Mn(I)):N:2,11,13:
: Rmerge v Resolution:N:2,4,5,7:
: Average I,sd and Sigma :A:2,9,10,12: : Fractional bias :A:2,17: $$
N 1/resol^2 Dmin(A) Rmrg  Rfull   Rcum  Ranom  NanomAv_I  SIGMA  
I/sigma   sd Mn(I/sd)  Nmeas  Nref  Ncent FRCBIAS  Nbias $$



  N 1/d^2 Dmin(A) Rmrg  Rfull   Rcum  Ranom  NanomAv_I  SIGMA I/ 
sigma   sd Mn(I/sd)  Nmeas   Nref  Ncent FRCBIAS  Nbias

$$
 1 0.0248  6.36  0.049   - 0.049   - 0   171815  17806
9.6  42009   7.3 3085 84481  -0.059899
 2 0.0495  4.49  0.068   - 0.058   - 092604  11948
7.8  22958   7.1 5715150884  -0.044   1765
 3 0.0743  3.67  0.113   - 0.080   - 0   136756  35595
3.8  33538   6.9 5188144655  -0.062   1499
 4 0.0990  3.18  0.161   - 0.099   - 080572  34834
2.3  21356   5.9 6512183257  -0.103   1898
 5 0.1238  2.84  0.129   - 0.102   - 035017   7334
4.8   9786   5.5 8897248481  -0.038   2663
 6 0.1485  2.59  0.192   - 0.107   - 017780   5282
3.4   6082   4.2 7234206957   0.002   2061
 7 0.1733  2.40  0.268   - 0.112   - 011018   4436
2.5   5042   3.4 8308238349  -0.033   2364
 8 0.1980  2.25  0.509   - 0.118   - 0 6611   5348
1.2   5286   2.2 6637192221  -0.016   1873
 9 0.2228  2.12  0.773   - 0.131   - 0 9030  33528
0.3   7036   1.6 66831941 6  -0.169   1906
10 0.2475  2.01  1.043   - 0.142   - 0 4970  10229
0.5   6723   1.4 7108208110  -0.201   2084

$$
bFor inline graphs use a Java browser/b/applet

Overall: 0.142   - 0.142   - 045355  19774
2.3  13412   4.165367   18510   501  -0.062  19012
  Rmrg  Rfull   Rcum  Ranom  NanomAv_I  SIGMA I/ 
sigma   sd Mn(I/sd)  Nmeas   Nref  Ncent FRCBIAS  Nbias





On 4 Aug 2009, at 09:47, Eleanor Dodson wrote:

Cant you read the shell limits off the loggraphs? The numbers in  
the tables are given as 4sin**2/Lamba**2 I think but that is  
converted to As in the loggraph.

Is that what you mean though?
Eleanor

Francis E Reyes wrote:

Hello ccp4'ers


Where is / how can I obtain the resolution shell for each  
resolution bin in scala? My eyes can't seem to find it.



Thanks


FR

-
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D




-
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D

Re: [ccp4bb] detergent crystals

2009-08-04 Thread Van Den Berg, Bert 
This has been elaborated before, but you can safely assume they are NOT 
detergent crystals. DDM may be harder to crystallize than your average membrane 
proteinI hope those crystals diffract!

Bert van den Berg
University of Massachusetts Medical School
Program in Molecular Medicine
Biotech II, 373 Plantation Street, Suite 115
Worcester MA 01605
Phone: 508 856 1201 (office); 508 856 1211 (lab)
e-mail: bert.vandenb...@umassmed.edu
http://www.umassmed.edu/pmm/faculty/vandenberg.cfm



-Original Message-
From: CCP4 bulletin board on behalf of Parveen Goyal
Sent: Tue 8/4/2009 11:10 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] detergent crystals
 
Hi All,

I got some hexagonal crystals in one of my crystal condition. The protein is
a membrane protein and contains 0.05% DDM. Has anybody seen DDM crysals and
if yes, how do they look like?

thanks in advance

Parveen Goyal