Dear Pramod, It's difficult to be certain based on what you have posted but my best guess would be problems with symmetry determination it's quite possible for pointless to be fooled into assigning higher symmetry if some form of pseudo-symmetry is present. What does the native Patterson look like? Any large off-origin peaks might give you a clue. The safest thing to do would be to integrate in P1 and attempt to carry out molecular replacement in P1 and see how that refines. Hopefully be able to determine the correct symmetry from this (Zanuda may well be able to help at this point!). Ed. -- Dr. E.D. Lowe Department of Biochemistry University of Oxford South Parks Road Oxford, UK OX1 3QU
e:[email protected] t: +44 (0) 1865 613288 f: +44 (0) 1865 613201 From: Pramod Kumar <[email protected]<mailto:[email protected]>> Reply-To: Pramod Kumar <[email protected]<mailto:[email protected]>> Date: Tue, 18 Jun 2013 02:58:36 +0530 To: <[email protected]<mailto:[email protected]>> Subject: Re: [ccp4bb] str solving problem Dear Abhinav I would suggest you integrate in p1 and run pointless. after integrating in p1 and running the pointless its still concluding the SG c2221. How do you determine the resolution cut off of 2.9A? the basis of resolution at 2.9A* was the completeness and I/Sigma value. Two molecule in ASU further supported by Matthews coefficient and solvent percentage content. Is this a homology model? or at least side chains replaced by correct ones, like with chainsaw? Have you trimmed loops and floppy regions in the model? its not homology model, I have used chainsaw to make the model for molecular replacement, and trimmed the model for floppy, loopy ambiguousness regions. plz see the snap shot of the model. thanks and regards... pramod On Tue, Jun 18, 2013 at 1:16 AM, Abhinav Kumar <[email protected]<mailto:[email protected]>> wrote: Hi Pramod, I would suggest you integrate in p1 and run pointless. If your Rfree is above 0.45, I wouldn't trust the model. How do you determine the resolution cut off of 2.9A? In MR, the score should improve when the program places the second copy to the first molecule. Is this a homology model? or at least side chains replaced by correct ones, like with chainsaw? Have you trimmed loops and floppy regions in the model? Thanks, Abhinav JCSG@SSRL, SLAC (650) 926-2992 On 06/17/2013 12:36 PM, Pramod Kumar wrote: Dear Abhinav Kumar thanks for kind suggestions I have tried as follow. 1. You should try to identify the correct space group first. *integration in p21 given the following statics in pointless Alternative reindexing Lklhd CC R(E^2) Number Cell_deviation [h,k,l] 0.566 0.957 0.094 25580 0.00 [l,-k,h] 0.434 0.853 0.195 25580 0.20 *integration in c2221 given the following statics in pointless Spacegroup TotProb SysAbsProb Reindex Conditions ( 20) 0.997 0.997 00l: l=2n (zone 1) moreover Zanuda and molrep's chekall space group option also suggests c2221, 2. A template with 31% identity is not a great model. The number of molecules in ASU will affect your chances of success.Hopefully it's not large. wrfac of 0.6 and Rfree of 0.5 suggest the solution may be incorrect. Did you try phaser? * this is the limitation of my data that came from three month old crystal, there are two molecules in ASU (what is the extant to say "reasonably good" please ?), initially phaser was failed, with the balbes output as ensemble it worked with following profile .. ** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.5.2 *** ************************************************************************************* Current is Best Solution (first) New Best LLG : 101.7 (8.70) Best Search Component so far: ensemble1 ************************************************************************************* *** Phaser Module: MOLECULAR REPLACEMENT REFINEMENT AND PHASING 2.5.2 *** ************************************************************************************* Resolution of All Data (Number): 2.91 47.64 (15877) Resolution of Selected Data (Number): 2.91 47.64 (15877) Refinement Table (Unsorted) --------------------------- #+ = input number #* = results number #+ #* (Initial LLG & Rval) (Refined LLG & Rval) Unique =# Tmplt SpaceGroup 1 1 908.3 48.8 1804.3 46.4 YES C 2 2 21 Refinement Table (Sorted) ------------------------- #+ = input number #* = results number #+ #* (Initial LLG & Rval) (Refined LLG & Rval) Unique =# Tmplt SpaceGroup 1 1 908.3 48.8 1804.3 46.4 YES C 2 2 21 but again the refmac is showing R factor 0.4404 0.4203 R free 0.4955 0.5027 Rms BondLength 0.0254 0.0093 Rms BondAngle 3.1234 1.4581 Rms ChirVolume 0.1741 0.0706 3. Did you check for twinning? TWINNING SUMMARY Twinning fraction from H-test: 0.00 L-statistic from L-Test: 0.48 Relation between L statistics and twinning fraction: Twinning fraction = 0.000 L statistics = 0.500: Twinning fraction = 0.100 L statistics = 0.440: Twinning fraction = 0.500 L statistics = 0.375: NO Twinning detected thanks and regards pramod... On Mon, Jun 17, 2013 at 10:15 PM, Abhinav Kumar <[email protected]<mailto:[email protected]>> wrote: Hi Pramod, 1. You should try to identify the correct space group first. Did you integrate in p1 and run pointless? 2. A template with 31% identity is not a great model. The number of molecules in ASU will affect your chances of success. Hopefully it's not large. wrfac of 0.6 and Rfree of 0.5 suggest the solution may be incorrect. Did you try phaser? 3. Did you check for twinning? Thanks, Abhinav JCSG@SSRL, SLAC (650) 926-2992 On 06/17/2013 09:35 AM, Pramod Kumar wrote: Dear group I have a crystal data diffracted around 2.9 A*, during the data reduction HKL2000 not convincingly showed the space group (indexed in lower symmetry p1), while the mosflm given C-centered Orthorhombic, and again with little play around HKL2000 given CO, now the model for molecular replacement with closest identity of 31 given a contrast of 2, score 0.30 and wrfac 0.60. but "balbes" uses different models with lesser identity, no matter which way I am going the rFree keep on increasing during refinement in refmac, when I build the model in coot with deletion and addition of residue it starts with relatively low but gradually rises through almost all cycles although model fits to the density well and residue are building, coot validation parameters are also reasonable OK for geometry, rotamer, density fit,.. now my question.... * where should i first check for possible correction? * In molecular replacement what should be the red line for identity and related criteria? * if initial rFree starts around 50, how likely that its not the right way? * my rms bond angle is close to 1 while the bond length is 0.01 and chiral 0.1 concludes what is serious? sincere apology for amateur query if any... thanks in advance pramod -- ************************************************ Pramod Kumar. Graduate Student. Crystallography lab. Department Of Biotechnology. Indian Institute Of Technology Roorkee Uttranchal.247667 India +919359189657. ************************************************ -- ************************************************ Pramod Kumar. Graduate Student. Crystallography lab. Department Of Biotechnology. Indian Institute Of Technology Roorkee Uttranchal.247667 India +919359189657. ************************************************
