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PDB ID Mentions in PubMed Central Article count: 1

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PDB ID Mentions in PubMed Central

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Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX.

(2012) Acta Crystallogr D Biol Crystallogr 68

PubMed: 22868759 | PubMedCentral: PMC3413210 | DOI: 10.1107/S0907444912017453

of residues Bond-length r.m.s.d. () Bond-angle r.m.s.d. () Side-chain planarity r.m.s.d. () -Angle standard deviation () R factor R free Clashes Severe clashes 2x3k 2.50 1145 0.019 2.3 0.005 8.0 0.212... 0.267 19 0 2xda 1.85 150 0.025 2.5 0.007 6.9 0.175 0.215 3 0 2xn8 1.64 409 0.022 2.2 0.005 6.6 0.170 0.221 2 0 2xpp 1.74 161 0.016 1.9 0.005 5.2 0.197 0.251 3 0 2xs6 2.09 166 0.019 2.0 0.004 6.8 0.195 0.263 1 0 2xsn 2.68 1341 0.017 2.0 0.005 6.6 0.229 0.275 16 0 2xsq 1.72 179 0.022 2.1 0.009 6.4 0.158 0.195 0 0 2xsw 1.90 666 0.021 2.3 0.007 7.0 0.166 0.211 5 0 2xsx 1.70 869 0.023 2.1 0.007 6.4 0.162 0.203 4 0 2xu7 1.90 752 0.020 2.2 0.006 8.0 0.186 0.235 1 0 2xul 2.20 645 0.016 2.2 0.003 7.2 0.189 0.231 1 0 2xvs 1.80 166 0.022 2.3 0.008 6.9 0.177 0.252 1 0 2xvv 2.40 582 0.019 2.3 0.005 6.8 0.182 0.245 3 0 2xxj 1.96 1239 0.017 1.9 0.007 6.5 0.179 0.241 8 0 3acw 1.63 284 0.019 2.0 0.009 5.8 0.201 0.242 1 0 3aey 1.92 698 0.021 2.2 0.008 6.3 0.171 0.204 12 0 3ajx 1.60 828 0.022 2.2 0.006 5.7 0.178 0.211 1 0 3ale 2.50 1460 0.015 2.1 0.004 7.5 0.233 0.272 16 0 3am9 2.17 2584 0.017 2.1 0.005 7.1 0.175 0.241 23 0 3l9w 1.75 695 0.023 2.4 0.009 6.5 0.199 0.233 3 0 3lb4 1.56 274 0.018 2.3 0.012 5.1 0.244 0.277 1 0 3lfl 2.10 686 0.017 1.9 0.003 8.5 0.202 0.269 8 0 3lje 1.75 121 0.025 2.4 0.006 6.5 0.175 0.211 1 0 3ljq 1.90 570 0.020 2.2 0.006 7.2 0.144 0.200 5 0 3lju 1.70 373 0.021 2.2 0.007 6.9 0.192 0.237 1 0 3lpf 2.26 1180 0.017 2.3 0.005 10.2 0.280 0.325 30 1 3lre 2.20 589 0.016 2.1 0.005 7.0 0.218 0.273 2 0 3lrp 2.50 181 0.017 2.2 0.004 7.1 0.184 0.252 3 0 3lt3 2.10 404 0.019 2.4 0.005 7.5 0.188 0.282 2 0 3m0e 2.63 1729 0.015 1.9 0.004 6.8 0.236 0.273 18 0 3m0h 1.58 1685 0.022 2.2 0.008 5.8 0.144 0.178 9 0 3m4z 1.94 309 0.020 2.1 0.007 6.1 0.160 0.203 0 0 3m5o 1.60 410 0.015 2.0 0.007 7.0 0.206 0.247 2 2 3m67 1.80 257 0.026 2.6 0.005 7.9 0.168 0.226 4 0 3mbv 2.00 222 0.017 1.8 0.006 5.9 0.248 0.292 1 0 3mfa 1.63 194 0.021 2.3 0.012 8.6 0.181 0.225 1 0 3mif 2.00 310 0.021 2.4 0.008 9.3 0.194 0.242 3 0 3mk9 2.08 173 0.017 1.9 0.006 6.8 0.186 0.246 2 0 3mke 1.75 265 0.020 2.1 0.010 6.8 0.148 0.191 0 0 3mvi 1.60 698 0.023 2.2 0.008 6.3 0.162 0.205 3 0 3mxe 1.85 198 0.019 2.3 0.005 7.7 0.183 0.251 0 0 3n2v 1.55 158 0.023 2.4 0.008 7.2 0.178 0.227 0 0 3nfy 1.94 498 0.017 2.1 0.004 6.9 0.181 0.259 6 0 3ni0 1.60 182 0.017 1.9 0.003 5.2 0.213 0.254 0 0 3nk4 2.00 581 0.021 2.5 0.006 7.8 0.217 0.247 7 0 3nl6 2.61 1545 0.016 2.4 0.005 7.8 0.225 0.273 23 2 3nm8 2.00 570 0.018 2.2 0.007 7.4 0.191 0.262 2 0 3nmi 2.01 636 0.023 2.4 0.005 6.8 0.198 0.244 9 1 3nof 1.60 213 0.021 2.4 0.010 6.5 0.186 0.216 2 0 3nok 1.65 466 0.016 2.0 0.005 7.4 0.198 0.243 4 0 3nv6 2.20 404 0.015 2.0 0.004 6.6 0.196 0.260 0 0 3nxg 1.95 1291 0.018 2.2 0.006 7.5 0.166 0.213 8 0 3nxp 2.20 363 0.015 2.1 0.005 8.1 0.196 0.238 9 0 3o0a 1.77 425 0.019 2.2 0.007 7.2 0.187 0.248 2 2 3o3p 1.70 635 0.020 2.5 0.006 8.2 0.216 0.251 14 0 3o4h 1.82 2302 0.015 2.2 0.005 6.5 0.216 0.270 16 2 3o79 1.60 202 0.024 2.5 0.012 11.1 0.192 0.239 2 1 3o86 1.60 709 0.021 2.1 0.007 6.8 0.167 0.196 4 0 3oae 2.80 2105 0.017 2.5 0.005 9.4 0.237 0.294 39 0 3oag 2.30 669 0.015 2.1 0.005 8.3 0.210 0.261 1 0 3oc2 1.97 495 0.019 2.3 0.007 7.5 0.171 0.226 5 1 3occ 1.70 1424 0.021 2.1 0.007 7.1 0.156 0.192 15 5 3oep 1.75 485 0.020 2.2 0.008 6.5 0.168 0.210 4 0 3oi7 2.40 1028 0.015 1.9 0.005 6.9 0.241 0.280 7 0 3oia 1.65 405 0.022 2.3 0.008 7.0 0.171 0.237 5 0 3olz 2.75 743 0.014 2.0 0.003 6.8 0.238 0.264 10 0 3om1 1.68 740 0.022 2.4 0.007 6.9 0.183 0.223 6 0 3onw 2.38 702 0.018 2.2 0.005 7.4 0.225 0.263 6 0 3orv 1.91 1707 0.017 2.0 0.006 7.2 0.155 0.207 10 0 3oux 2.40 550 0.017 2.2 0.004 6.4 0.220 0.267 8 0 3p10 1.70 471 0.018 2.1 0.006 6.3 0.173 0.222 4 0 3p14 2.51 1608 0.015 2.1 0.005 7.1 0.211 0.259 21 5 3p1a 1.70 281 0.023 2.0 0.009 5.8 0.162 0.212 2 0 3p1m 2.54 1017 0.013 2.1 0.002 6.9 0.231 0.273 8 0 3p2e 1.68 402 0.021 2.2 0.008 6.6 0.186 0.234 3 0 3p32 1.90 306 0.024 2.3 0.005 7.3 0.204 0.252 3 0 3p4i 2.35 760 0.019 2.1 0.004 7.0 0.195 0.241 2 0 3p4l 1.80 198 0.018 2.0 0.008 7.2 0.200 0.248 1 0 3p5o 1.60 127 0.023 2.1 0.008 6.1 0.156 0.209 1 0 3p5t 2.70 1653 0.016 2.0 0.004 7.4 0.230 0.285 4 0 3p77 1.60 371 0.021 2.3 0.008 6.8 0.173 0.221 2 0 3p7h 2.30 520 0.016 2.0 0.005 8.1 0.200 0.244 2 0 3p8s 2.00 302 0.018 2.2 0.006 7.7 0.165 0.221 2 0 3paj 2.00 599 0.018 2.2 0.006 6.2 0.179 0.251 6 0 3pde 1.75 1149 0.020 2.1 0.006 6.1 0.169 0.212 8 0 3pdt 1.80 251 0.018 2.0 0.005 7.6 0.182 0.237 2 0 3peh 2.75 523 0.019 2.6 0.006 8.4 0.234 0.288 10 0 3pgj 2.49 1075 0.014 1.9 0.003 7.0 0.249 0.287 3 0 3pgy 1.92 1609 0.017 2.0 0.005 6.7 0.173 0.225 8 0 3ph7 2.50 1376 0.016 2.0 0.006 6.4 0.248 0.304 8 0 3phe 2.20 2232 0.016 2.0 0.004 7.7 0.213 0.255 11 1 3pj9 2.10 549 0.021 2.2 0.004 7.3 0.185 0.220 10 0 3pjp 1.60 389 0.022 2.4 0.008 7.7 0.203 0.253 2 0 3pk0 1.74 1043 0.023 2.3 0.007 6.2 0.160 0.207 7 0 Total   66891             573 23 Mean 1.99   0.019 2.2 0.006 7.1 0.193 0.242     No.

Wang, D. Moras, G. Eriani J. Cavarelli (unpublished work) 3o3p 1.70 635 PHENIX 0.007 1.1 0.002 5.2 0.221 0.255 39 4 Empadinhas et al. (2011 ▶ ) 3o4h 1.82 2302 REFMAC 0.019 1.7 0.007 6.2 0.244 0.267 71 19 Harmat et al. (2011 ▶ ) 3o79 1.60 202 REFMAC 0.022 1.7 0.009 5.3 0.210 0.237 4 2 Khan et al. (2010 ▶ ) 3o86 1.60 709 PHENIX 0.010 1.3 0.004 5.8 0.173 0.198 17 0 Eidam et al. (2010 ▶ ) 3oae 2.80 2105 CNS 0.011 1.5 0.006 1.4 0.272 0.288 238 40 Dasgupta et al. (2011 ▶ ) 3oag 2.30 669 REFMAC 0.009 1.2 0.003 7.8 0.208 0.262 13 2 Corminboeuf et al. (2010 ▶ ) 3oc2 1.97 495 PHENIX 0.007 1.1 0.002 5.4 0.181 0.223 21 3 Sainsbury et al. (2010 ▶ ) 3occ 1.70 1424 REFMAC 0.015 1.5 0.010 6.6 0.169 0.197 29 8 New York SGX Research Center for Structural Genomics (unpublished work) 3oep 1.75 485 REFMAC 0.006 1.1 0.003 5.4 0.191 0.215 0 0 Jacques et al. (2011 ▶ ) 3oi7 2.40 1028 REFMAC 0.012 1.3 0.003 5.9 0.237 0.269 19 8 Clasquin et al. (2011 ▶ ) 3oia 1.65 405 REFMAC 0.011 1.3 0.004 5.7 0.191 0.241 6 0 Lee et al. (2011 ▶ ) 3olz 2.75 743 PHENIX 0.006 0.9 0.002 5.0 0.211 0.265 26 1 Kumar Mayer (2010 ▶ ) 3om1 1.68 740 PHENIX 0.006 1.0 0.002 5.0 0.193 0.224 14 1 Kumar Mayer (2010 ▶ ) 3onw 2.38 702 REFMAC 0.009 1.1 0.002 5.1 0.251 0.280 13 1 Bosch et al. (2011 ▶ ) 3orv 1.91 1707 REFMAC 0.025 1.9 0.009 6.4 0.171 0.212 22 1 Abu Tarboush et al. (2010 ▶ ) 3oux 2.40 550 PHENIX 0.008 1.1 0.002 4.7 0.219 0.285 35 3 Sun Weis (2011 ▶ ) 3p10 1.70 471 REFMAC 0.012 1.3 0.004 5.2 0.184 0.218 7 0 Begley et al. (2011 ▶ ) 3p14 2.51 1608 REFMAC 0.019 1.8 0.005 6.5 0.201 0.266 108 22 T. T. N. Doan, P. Prabhu, J. K. Lee, L. W. Wang, J. K. Kim, M. Jeya Y. J. Ahn (unpublished work) 3p1a 1.70 281 REFMAC 0.015 1.5 0.006 5.1 0.169 0.211 4 0 Structural Genomics Consortium (unpublished work) 3p1m 2.54 1017 REFMAC 0.013 1.3 0.003 5.8 0.240 0.270 28 2 Structural Genomics Consortium (unpublished work) 3p2e 1.68 402 CNS 0.005 1.2 0.005 1.4 0.207 0.244 16 0 Husain et al. (2011 ▶ ) 3p32 1.90 306 REFMAC 0.015 1.3 0.004 5.6 0.226 0.254 3 0 Seattle Structural Genomics Center for Infectious Disease (unpublished work) 3p4i 2.35 760 REFMAC 0.016 1.5 0.003 5.7 0.200 0.244 11 0 Seattle Structural Genomics Center for Infectious Disease (unpublished work) 3p4l 1.80 198 CNS 0.010 1.6 0.008 2.2 0.205 0.240 7 2 Yang et al. (2011 ▶ ) 3p5o 1.60 127 REFMAC 0.007 1.0 0.003 4.9 0.179 0.207 1 0 Nicodeme et al. (2010 ▶ ) 3p5t 2.70 1653 REFMAC 0.010 1.3 0.003 6.1 0.225 0.272 179 33 Li, Tong et al. (2011 ▶ ) 3p77 1.60 371 REFMAC 0.012 1.4 0.005 6.1 0.194 0.226 2 0 Hee et al. (2010 ▶ ) 3p7h 2.30 520 REFMAC 0.110 1.2 0.004 6.5 0.204 0.245 16 2 Chatwell et al. (2008 ▶ ) 3p8s 2.00 302 REFMAC 0.010 1.2 0.003 6.2 0.192 0.226 3 0 U. Sharma, N. Ahmed, M. V. Krishnasastry C. G. Suresh (unpublished work) 3paj 2.00 599 REFMAC 0.009 1.2 0.007 2.0 0.213 0.259 20 2 Center for Structural Genomics of Infectious Diseases (unpublished work) 3pde 1.75 1149 REFMAC 0.013 1.6 0.004 5.0 0.177 0.209 17 0 New York SGX Research Center for Structural Genomics (unpublished work) 3pdt 1.80 251 REFMAC 0.011 1.3 0.003 5.9 0.202 0.247 4 0 Crawley et al. (2011 ▶ ) 3peh 2.75 523 REFMAC 0.013 1.7 0.007 2.5 0.236 0.279 8 1 Structural Genomics Consortium (unpublished work) 3pgj 2.49 1075 REFMAC 0.007 1.4 0.004 0.9 0.238 0.279 40 1 Center for Structural Genomics of Infectious Diseases (unpublished work) 3pgy 1.92 1609 REFMAC 0.017 1.5 0.006 5.7 0.190 0.227 29 2 Center for Structural Genomics of Infectious Diseases (unpublished work) 3ph7 2.50 1376 BUSTER 0.014 1.7 0.008 2.4 0.249 0.291 11 0 Artz et al. (2011 ▶ ) 3phe 2.20 2232 CNX 0.004 0.7 0.003 5.1 0.222 0.265 131 15 Kumar et al. (2011 ▶ ) 3pj9 2.10 549 REFMAC 0.017 1.5 0.005 6.2 0.206 0.221 16 2 Center for Structural Genomics of Infectious Diseases (unpublished work) 3pjp 1.60 389 PHENIX 0.006 1.0 0.003 5.6 0.214 0.251 5 0 Sun et al. (2010 ▶ ) 3pk0 1.74 1043 REFMAC 0.017 1.5 0.007 5.5 0.184 0.210 5 0 Seattle Structural Genomics Center for Infectious Disease (unpublished work) Total   66891               2639 349   Mean       0.014 1.4 0.005 5.1 0.207 0.243       No.

Publication Year: 2012