Hi Sneha, typical R-factors at this resolution are (using "phenix.r_factor_statistics 1.9" command): Histogram of Rwork for models in PDB at resolution 1.80-2.00 A: 0.093 - 0.118 : 4 0.118 - 0.143 : 216 0.143 - 0.168 : 2142 0.168 - 0.193 : 5011 0.193 - 0.218 : 3592 0.218 - 0.243 : 1090 <<< your case 0.243 - 0.268 : 151 0.268 - 0.293 : 20 0.293 - 0.319 : 1 0.319 - 0.344 : 3 Histogram of Rfree for models in PDB at resolution 1.80-2.00 A: 0.138 - 0.163 : 40 0.163 - 0.189 : 651 0.189 - 0.214 : 3178 0.214 - 0.240 : 4512 0.240 - 0.265 : 2809 <<< your case 0.265 - 0.290 : 854 0.290 - 0.316 : 159 0.316 - 0.341 : 22 0.341 - 0.367 : 3 0.367 - 0.392 : 2 Histogram of Rfree-Rwork for all model in PDB at resolution 1.80-2.00 A: 0.000 - 0.010 : 97 0.010 - 0.020 : 683 0.020 - 0.030 : 2367 0.030 - 0.040 : 3800 <<< your case 0.040 - 0.050 : 3085 0.050 - 0.060 : 1422 0.060 - 0.070 : 511 0.070 - 0.080 : 172 0.080 - 0.090 : 73 0.090 - 0.100 : 20 Number of structures considered: 12230 ..so, in terms of R-factors your are fine. Run Comprehensive validation in Phenix GUI and check all "red flags". I would say you need to be able to explain rotamer/Ramachandran outliers or fix them otherwise. Pavel On 10/24/14 11:50 AM, Sneha Rangarajan wrote:
Hi everyone,
For a 1.9A dataset, here are my statistics-
Rfactors: 22/26
Ramachandran favored: 90.60%
Ramachandran outliers: 2.17%
Rotamer outliers: 4%
Clashscore: 8
Bonds: 0.007
Angles: 1.2
I have tried a couple of things to refine it further but nothing seems to improve all the parameters.
My question is what is an acceptable Rfactor at this resolution for deposition in pdb?
Thanks,
Sneha