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PDB ID Mentions in PubMed Central Article count: 3

Citations in PubMed

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PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Super-resolution biomolecular crystallography with low-resolution data.

(2010) Nature 464

PubMed: 20376006 | PubMedCentral: PMC2859093 | DOI: 10.1038/nature08892

Table 2 DEN Refinement Improves Low Resolution Structures in the PDB a R free R free -R work Ramachandran Score PDB Identifier Resolution(Å) Number Residues DEN noDEN Improvement DEN noDEN DEN... noDEN Improvement Comments 1av1 4.00 804 0.335 0.336 0.0012 0.07 0.07 0.840 0.872 −0.0314 1isr 4.00 448 0.233 0.237 0.0043 0.07 0.07 0.833 0.833 0.0000 1jl4 4.30 557 0.353 0.354 0.0009 0.12 0.11 0.718 0.705 0.0127 1pgf 4.50 1102 0.284 0.295 0.0108 0.08 0.11 0.856 0.804 0.0519 Small differences throughout 1r5u 4.50 3517 0.334 0.335 0.0003 0.05 0.05 0.714 0.710 0.0046 1xdv 4.10 1517 0.358 0.367 0.0089 0.12 0.11 0.780 0.783 −0.0034 1xxi 4.10 3532 0.407 0.465 0.0582 0.05 0.12 0.842 0.612 0.2301 Large differences (~ 4 A domain motions) 1ye1 4.50 574 0.312 0.350 0.0381 0.08 0.15 0.894 0.705 0.1890 Small differences throughout 1yi5 4.20 1356 0.323 0.336 0.0139 0.07 0.09 0.758 0.709 0.0497 Local differences in several chains 1z9j 4.50 821 0.317 0.331 0.0135 0.07 0.09 0.838 0.762 0.0761 Large differences in chain A (domain motion) 2a62 4.50 319 0.340 0.353 0.0131 0.07 0.09 0.590 0.606 −0.0159 2bf1 4.00 304 0.479 0.492 0.0131 0.12 0.12 0.467 0.507 −0.0400 2i36 4.10 962 0.387 0.401 0.0137 0.02 0.03 0.839 0.687 0.1520 Local difference in chain B 2qag 4.00 702 0.392 0.401 0.0091 0.02 0.02 0.616 0.614 0.0016 2vkz 4.00 10941 0.327 0.337 0.0095 0.05 0.07 0.832 0.762 0.0692 Large differences in subdomain placements 3bbw 4.00 543 0.304 0.334 0.0304 0.01 0.04 0.876 0.776 0.0998 Significant local difference 3crw 4.00 485 0.324 0.338 0.0136 0.09 0.11 0.836 0.777 0.0589 Large difference in one domain (hinge motion) 3dmk 4.19 2127 0.407 0.428 0.0211 0.08 0.11 0.742 0.653 0.0896 Differences throughout, reference model only 50% 3du7 4.10 1839 0.332 0.336 0.0039 0.09 0.09 0.730 0.707 0.0225 Average 4.19 1708 0.345 0.359 0.0146 0.07 0.09 0.768 0.715 0.0535 Minimum 4.00 304 0.233 0.237 0.0003 0.01 0.02 0.467 0.507 −0.0400 Maximum 4.50 10941 0.479 0.492 0.0582 0.12 0.15 0.894 0.872 0.2301 a Nineteen PDB structures were re-refined with and without DEN ( Online Methods ).

Publication Year: 2010


The linker domain of basal transcription factor TFIIB controls distinct recruitment and transcription stimulation functions.

(2011) Nucleic Acids Res 39

PubMed: 20851833 | PubMedCentral: PMC3025549 | DOI: 10.1093/nar/gkq809

( B ) Alignment of the TFIIB structures of three yeast RNAP–TFIIB co-crystals [PDB codes 3K7A (blue) ( 14 ), 3K1F (purple) ( 15 ) and 1R5U (black) ( 13 )] superimposed on the RNAP active centr... domains and nucleic acids (PDB code: 2E2H).

Publication Year: 2011


Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution.

(2012) Acta Crystallogr D Biol Crystallogr 68

PubMed: 22505258 | PubMedCentral: PMC3322597 | DOI: 10.1107/S0907444911047834

    R free R free R work Ramachandran score PDB entry Resolution () PHENIX PHENIX with reference DEN † PHENIX PHENIX with reference DEN † PHENIX PHENIX with reference D... N † 1av1 ‡ 4.00 0.343 0.342 0.335 0.11 0.08 0.07 0.462 0.898 0.840 1jl4 4.30 0.344 0.320 0.353 0.11 0.08 0.12 0.655 0.803 0.718 1r5u 4.50 0.248 0.245 0.334 0.05 0.04 0.05 0.627 0.896 0.714 1xdv 4.10 0.345 0.348 0.358 0.11 0.11 0.12 0.758 0.833 0.780 1xxi 4.10 0.297 0.278 0.407 0.09 0.06 0.05 0.538 0.958 0.842 1ye1 4.50 0.318 0.289 0.312 0.16 0.12 0.08 0.818 0.975 0.894 1yi5 4.20 0.317 0.284 0.323 0.10 0.06 0.07 0.608 0.944 0.758 1z9j 4.50 0.236 0.229 0.317 0.08 0.07 0.07 0.593 0.952 0.838 2a62 4.50 0.371 0.354 0.340 0.14 0.11 0.07 0.629 0.749 0.590 2bf1 ‡ 4.00 0.421 0.432 0.479 0.07 0.05 0.12 0.480 0.666 0.467 2i36 4.10 0.412 0.403 0.387 0.09 0.06 0.02 0.568 0.889 0.839 2qag 4.00 0.378 0.379 0.392 0.04 0.04 0.02 0.471 0.781 0.616 2vkz ‡ 4.00 0.278 0.272 0.327 0.08 0.07 0.05 0.770 0.969 0.832 3bbw 4.00 0.321 0.305 0.304 0.08 0.05 0.01 0.806 0.942 0.876 3crw 4.00 0.339 0.292 0.324 0.10 0.06 0.09 0.781 0.872 0.836 3dmk 4.19 0.292 0.282 0.407 0.12 0.09 0.08 0.707 0.827 0.742 3du7 4.10 0.304 0.302 0.332 0.10 0.07 0.09 0.553 0.838 0.730 Average 4.18 0.327 0.315 0.355 0.096 0.072 0.069 0.637 0.870 0.760 † Data taken from Table 2 in Schrder et al. (2010 ▶ ).

There were seven cases in which reference-model restraints resulted in a lower clashscore than DEN restraints ( 1r5u , 1xxi , 1ye1 , 1yi5 , 2vkz , 3bbw and 3dmk ).

Publication Year: 2012