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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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Experiences with archived raw diffraction images data: capturing cisplatin after chemical conversion of carboplatin in high salt conditions for a protein crystal.

(2013) J Synchrotron Radiat 20

PubMed: 24121332 | PubMedCentral: PMC3795548 | DOI: 10.1107/S0909049513020724

F o  −  F c density OMIT maps (green) and anomalous difference density (orange) maps at the 3σ cut-off level for ( a ) and ( b ) 4dd7 processed by XDS and EVAL , ( c ) ... nd ( d ) 4dd9 processed by XDS and EVAL and ( e ) and ( f ) 4g4c processed by XDS and EVAL , respectively.

This information, using both EVAL and XDS processing programs for each dataset ( 4dd7 , 4dd9 and 4g4c ), is given in Tables 2 ▶ and 3 ▶ .

Thus, using XDS to process these archived raw diffraction images (PDB ID 4dd7 / 4dd9 / 4g4c ), clearly significant anomalous difference density peaks in the carboplatin binding site were seen; appropriately placed for where a Cl atom in cisplatin would be expected to be for the Nδ binding site and for two Cl atoms in the N∊ binding site.

Whereas for 4dd9 and 4g4c , the anomalous difference density peaks are weaker, and thus harder to determine that the Cl atoms are in fact present.

Whereas, for 4dd9 and 4g4c , there is no evidence for all of these Cl atoms above our 3σ cut-off level, with only one Cl in the N∊ binding site being present above the 3σ cut-off level.

All of the raw diffraction images data can be found at , except for 4g4c , which are at , and now also mirrored at the Tardis Raw Data Archive in Australia ( ).

PDB IDs: 4dd0 , 4dd1 , 4dd2 , 4dd3 , 4dd4 , 4dd6 , 4dd7 , 4dd9 , 4dda , 4ddb , 4ddc , 3txb , 3txd , 3txe , 3txi , 3txj , 3txk , 3txf , 3txg , 3txh , 4g49 , 4g4a , 4g4b , 4g4c , 4g4h .

Publication Year: 2013

Carboplatin binding to histidine.

(2014) Acta Crystallogr F Struct Biol Commun 70

PubMed: 25195881 | PubMedCentral: PMC4157408 | DOI: 10.1107/S2053230X14016161

Reviewing those results along with our previous publication of the carboplatin-bound structures in DMSO medium studied at cryo and room temperatures (Tanley, Schreurs, Kroon-Batenburg & Helliw... ll, 2012 ▶ ; Tanley, Schreurs, Kroon-Batenburg, Meredith et al. , 2012 ▶ ; PDB entries 4dd7 , 4dd9 and 4g4c ), it was noted that there were two small extra anomalous difference electron-density peaks within the carboplatin binding sites (Tanley, Diederichs et al. , 2013 ▶ a ).

Publication Year: 2014

Experiences with making diffraction image data available: what metadata do we need to archive?

(2014) Acta Crystallogr D Biol Crystallogr 70

PubMed: 25286836 | PubMedCentral: PMC4187998 | DOI: 10.1107/S1399004713029817

These were the data sets with PDB codes 4dd9 (Rigaku R-AXIS images) and 4dd7 (Bruker PLATINUM 135 images with kappa goniometer) from Tanley, Schreurs et al. (2013 ▶ ) and data set 4g4c from Ta... ley et al. (2012 ▶ ).

Data set 4g4c is from an APEX2 detector (nonbinned), 60 pixels cm −1 , 1024 × 1024 pixels with a fixed-χ goniometer.

As an example of how difficult the interpretation of incomplete and inaccurate metadata can be when trying to read raw images, we compile the discussion that K. Diederichs (KD), L. Kroon-Batenburg (LKB) and A. Schreurs (AS) had with respect to the 4g4c data in the Supporting Information 1 .

Publication Year: 2014