1. I would recommend to use Molprobity on the website: http://molprobity.biochem.duke.edu/
2. Remember that if your spacegroup is P1, the origin (i.e. translations along a, b and c) is not determined and the first molecule may be placed anywhere. Similarly, in monoclinic spacegroups, the translation along b. is not determined.
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3, Campus Cantoblanco
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/content/research/macromolecular/mvraaij
On 9 Jun 2011, at 09:46, Ting-Wei Jiang wrote:
> Dear experts,
> I got two questions regarding refinement and structure determination by MR.
>
> 1.I got a dataset of resolution at 2A refined to Rvalue~20% and Rfree~24%
> I want to know if there is any program in CCP4 could help me to check the refined structure in detail.
> For example,the model statistics in CNS could list some information that infer band,angle violation...etc
> Or I should ask what do I need to check before submitting to PDB.
>
> 2.A dataset of resolution collected to 2.2A is from native protein crystal(A) and its complex form(A'+B)
> whose PDB code is 2QN5 was already determined by MR(use another protein as search model).I planned
> to use A' as search model but the A' looks broken.
> This number of molecules in AU was predicted to 4~6 using Mathews coefficient.
> N/a M.C. solvent%
> 4 2.99 58.92
> 5 2.39 48.65
> 6 1.99 38.38
> The coordinate or orientation of output pdb(as attached figure) from MR are always different since I changed
> parameter,such as different resolution,Multi copy,search mode...etc. even the contrast value of every run
> is pretty high(>>3)
> I really don't what happened with this dataset and any suggestion would be greatly appreciated.
>
>
> <output-pdb.png>
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