Re: [ccp4bb] how to improve Rfree?

[Pavel Afonine]

Hi Sivia, you say the resolution is 1.8A, and your R-work=0.19 and R-free=0.27. Here is the distribution of R-factors for structures in PDB deposited at similar resolution (in range between 1.75A and 1.85A): Histogram of Rwork for all model in PDB at resolution 1.75-1.85:      0.114 - 0.130      : 6      0.130 - 0.147      : 48      0.147 - 0.163      : 221      0.163 - 0.180      : 484      0.180 - 0.196      : 718  <<< your structure      0.196 - 0.212      : 508      0.212 - 0.229      : 271      0.229 - 0.245      : 105      0.245 - 0.262      : 20      0.262 - 0.278      : 7 Histogram of Rfree for all model in PDB at resolution 1.75-1.85:      0.153 - 0.171      : 17      0.171 - 0.190      : 127      0.190 - 0.208      : 380      0.208 - 0.227      : 647      0.227 - 0.245      : 648      0.245 - 0.263      : 360      0.263 - 0.282      : 132  <<< your structure      0.282 - 0.300      : 64      0.300 - 0.319      : 10      0.319 - 0.337      : 3 Histogram of Rfree-Rwork for all model in PDB at resolution 1.75-1.85:      0.001 - 0.013      : 41      0.013 - 0.025      : 336      0.025 - 0.036      : 852      0.036 - 0.048      : 693      0.048 - 0.060      : 309      0.060 - 0.072      : 98      0.072 - 0.084      : 40  <<< your structure      0.084 - 0.095      : 11      0.095 - 0.107      : 4      0.107 - 0.119      : 4 You also mentioned you cut the data off (the actual resolution is 1.6A). Doing so just to improve R-factor doesn't seem like a good idea. Similar histograms for structures at around 1.6A resolution: Histogram of Rwork for all model in PDB at resolution 1.55-1.65:      0.099 - 0.119      : 5      0.119 - 0.138      : 26      0.138 - 0.158      : 132      0.158 - 0.177      : 349      0.177 - 0.197      : 447  <<< your structure      0.197 - 0.217      : 281      0.217 - 0.236      : 129      0.236 - 0.256      : 17      0.256 - 0.275      : 6      0.275 - 0.295      : 1 Histogram of Rfree for all model in PDB at resolution 1.55-1.65:      0.137 - 0.156      : 6      0.156 - 0.175      : 45      0.175 - 0.195      : 208      0.195 - 0.214      : 391      0.214 - 0.233      : 395      0.233 - 0.253      : 200      0.253 - 0.272      : 96  <<< your structure      0.272 - 0.291      : 37      0.291 - 0.311      : 12      0.311 - 0.330      : 3 Histogram of Rfree-Rwork for all model in PDB at resolution 1.55-1.65:      0.001 - 0.010      : 27      0.010 - 0.019      : 217      0.019 - 0.029      : 374      0.029 - 0.038      : 350      0.038 - 0.047      : 233      0.047 - 0.056      : 106      0.056 - 0.065      : 49      0.065 - 0.075      : 23      0.075 - 0.084      : 10  <<< your structure      0.084 - 0.093      : 4 Pavel. On 10/19/09 5:49 AM, Sylvia Fanucchi wrote: Dear all I have been refining my structure using refmac5 restrained refinement and the model currently has an R-factor of 0.19. What is concerning me is that there is quite a big discrepancy between the Rfree and the R-factor, with the Rfree being around 0.27. Furthermore, after about 10 rounds of refinement, the R-free actually starts to increase slightly although the R-factor continues to decrease. Does this mean that there is significant bias in my model? Does anybody know how I could go about addressing this problem? Thanks for any help J Sylvia Fanucchi Ph.D Protein Structure-Function Research Unit East Campus, Gate House Room 416 School of Molecular and Cell Biology University of the Witwatersrand Johannesburg 2050 South Africa Tel: +27 (11) 717-6348 Fax: +27 (11) 717-6351 E-mail: sylvia.fanuc...@wits.ac.za    This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorized signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary.