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PDB ID Mentions in PubMed Central Article count: 4

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PDB ID Mentions in PubMed Central

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Experience with exchange and archiving of raw data: comparison of data from two diffractometers and four software packages on a series of lysozyme crystals.

(2013) J Appl Crystallogr 46

PubMed: 23396873 | PubMedCentral: PMC3547227 | DOI: 10.1107/S0021889812044172

1: 4dd0 ; 2: 4dd2 ; 3: 4dd3 ; 4: 4dd9 ; 5: 4dd1 ; 6: 4dd4 ; 7: 4dd6 ; 8: 4dd7 ; 9: 4ddc ; 10: 4dda ; 11: 4ddb .

1: 4dd0 ; 2: 4dd2 ; 3: 4dd3 ; 4: 4dd9 ; 5: 4dd1 ; 6: 4dd4 ; 7: 4dd6 ; 8: 4dd7 ; 9: 4ddc ; 10: 4dda ; 11: 4ddb .

A projection of reflections rejected by SADABS onto the detector ( 4dd7 ; Fig. 5 ▶ b ) shows that many occur in these areas of moisture, indicating systematic problems with the flood-field correction now not being appropriate as it would have been measured before the moisture build up.

Processed and derived data have been deposited with the PDB [PDB codes 3txb , 3txd , 3txe , 3txf , 3txg , 3txh , 3txi , 3txj and 3txk (new to this paper); PDB codes 4dd0 , 4dd1 , 4dd2 , 4dd3 , 4dd4 , 4dd6 , 4dd7 , 4dd9 , 4dda , 4ddb , 4ddc (from Tanley et al. , 2012 ▶ )].

1: 4dd0 ; 2: 4dd2 ; 3: 4dd3 ; 4: 4dd9 ; 5: 4dd1 ; 6: 4dd4 ; 7: 4dd6 ; 8: 4dd7 ; 9: 4ddc ; 10: 4dda ; 11: 4ddb .

Crystal 5 6 7 PDB code   4dd1   3txf 4dd4   3txg 4dd6   Software PROTEUM2 EVAL Mosflm PROTEUM2 EVAL Mosflm PROTEUM2 EVAL Mosflm Unit cell † a = 78.78 a = 78.88 a = 78.72 a = 78.44 a = 78.83 a = 79.11 a = 78.08 a = 78.01 a = 78.05   c = 37.28 b = 78.70 c = 37.29 c = 36.97 c = 37.02 c = 37.06 c = 37.11 c = 37.07 c = 37.08     c = 37.07               Observed reflections 118456 131592 87575 176370 173061 173696 320101 272733 248797 Unique reflections 11366 25216 9476 13407 11859 18753 13147 10901 9458 Resolution () 35.231.80 (1.891.80) 18.041.70 (1.761.70) 19.091.83 (1.931.83) 55.471.69 (1.791.69) 18.921.70 (1.761.70) 17.63 1.52 (1.621.52) 37.101.70 (1.801.70) 18.921.70 (1.761.70) 18.931.83 (1.931.83) Completeness (%) 99.9 (100) 97.7 (92.2) 86.9 (79.3) 95.9 (75.2) 88.6 ‡ (100) 69.11 (83.5) 99.6 (97.5) 82.8 ‡ (100) 88.5 (77.4) R merge 0.094 (0.278) 0.06 (0.200) 0.108 (0.28) 0.116 (0.357) 0.079 (0.313) 0.076 (1.33) 0.060 (0.286) 0.067 (0.306) 0.068 (0.22) Merged mean I / 18.8 (5.71) 16.9 (4.97) 12.6 (4.2) 20.8 (7.82) 22.8 (4.8) 7.7 (0.60) 31.5 (5.48) 34.5 (8.0) 40.1 (11.0) Redundancy 10.4 (7.9) 5.4 (4.4) 9.24 (6.7) 13.1 (5.9) 14.6 (9.1) 9.26 (3.2) 24.3 (16.2) 25.0 (18.0) 26.3 (19.1) B Wilson 15.8 15.1 13.9 14.3 14.0 15.2 14.3 15.7 13.5 Average atomic B factor () 22.3 15.7 17.4 23.6 14.0 21.5 17.9 14.7 14.6 R factor/ R free (%) 17.7/23.1 18.8/22.4 19.6/25.9 17.9/23.9 20.2/25.9 22.1/25.8 18.1/23.9 21.4/26.5 19.5/26.3 R factor (all) 18.1 19.1 19.9 20.8 20.5 22.3 18.5 21.6 19.8 R.m.s.d. bond lengths ()/angles () 0.0267/2.1128 0.020/2.043 0.0191/3.3062 0.0207/2.1302 0.018/1.861 0.0221/1.7157 0.0261/2.2494 0.0183/2.134 0.0176/2.1269 Crystal 8 9 PDB code 3txh 4dd7     4ddc   Software PROTEUM2 EVAL Mosflm PROTEUM2 EVAL Mosflm Unit cell † a = 78.84 a = 78.82 a = 78.80 a = 78.60 a = 78.94 a = 78.49   c = 37.03 c = 37.02 c = 37.00 c = 37.01 b = 79.08 c = 36.94           c = 36.98   Observed reflections 361272 500514 323705 30705 329619 209107 Unique reflections 13494 15970 12839 4377 21884 11716 Resolution () 55.751.69 (1.791.69) 20.671.60 (1.651.60) 19.111.72 (1.821.72) 54.451.54 (2.372.25) 19.161.80 (1.861.80) 18.721.72 (1.821.72) Completeness (%) 99.8 (99.4) 99.9 (99.9) 99.9 (100) 100 (100) 99.9 (100) 92.3 (99.1) R merge 0.0557 (0.156) 0.057 (0.179) 0.059 (0.15) 0.106 (0.583) 0.079 † (0.213) 0.15 (0.74) Merged mean I / 44.8 (10.7) 42.5 (7.0) 41.4 (9.9) 20.53 (23.18) 22.9 † (4.4) 12.0 (1.8) Redundancy 26.7 (9.8) 31.4 (9.4) 25.2 (9.4) 19.8 (3.91) 15.1 (5.6) 17.8 (6.2) B Wilson 12.2 12.5 12.2 8.4 15.1 15.7 Average atomic B factor () 15.8 13.6 13.7 16.2 16.2 30.2 R factor/ R free (%) 16.7/23.2 18.3/22.3 17.0/22.7 18.1/27.1 21.8/25.5 20.1/29.0 R factor (all) 16.9 18.5 17.3 19.2 21.9 20.6 R.m.s.d. bond lengths ()/angles () 0.0307/2.5650 0.0200/2.0684 0.0210/2.0594 0.0274/2.3062 0.0181/1.8160 0.0165/1.5159 The resolution was cut back because at higher resolutions the protein structure refinement gave poor R / R free statistics.

Table 1 Data collection strategies (from Tanley et al. , 2012 ▶ )   Detector distance (mm) Swing () Sweep () Rotation/frame () Generator filament current (mA) Rigaku R-AXIS IV     4dd0 (3txb) 100 0 360 1 20 4dd2 (3txd) 120 0 360 1 20 4dd3 (3txe) 120 0 272 1 20 4dd9 (3txi) 120 0 361 1 20 4dda (3txj) 135 0 181 1 20 4ddb (3txk) 200 0 360 1 20   Bruker PLATINUM 135     4dd1 60 † 20 307.0 0.5 60 4dd4 (3txf) 50 † 15.5 202.0 0.5 60 8.0 38.0 12.0 35.0 22.0 52.0 22.0 63.0 4dd6 (3txg) 60 † 20 360.0 0.5 60 20 360.0 4dd7 (3txh) 50 † 0 31.0 0.5 60 0 180.0 0 360.5 20 360.5 4ddc 50 † 0 360.0 0.5 60 20 360.0 † Distance from face of the detector to the phosphor plane is an additional 6.6mm.

Publication Year: 2013


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

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.

These confirm that, for 4dd7 , anomalous difference density for these Cl atoms are seen and should have been noted previously and, also, this dataset shows the most conversion of carboplatin to cisplatin based on the correlation coefficients out of OVERLAPMAP (Table 2 ▶ ).

Comparing these anomalous difference density peak heights with the peak heights from the EVAL (Schreurs et al. , 2010 ▶ ), MOSFLM (Leslie, 1999 ▶ ) and PROTEUM/D*Trek (Bruker, 2006 ▶ ; Pflugrath, 1999 ▶ ) processing programs (Tanley et al. , 2013 a ▶ ) (Table 1 ▶ ), it was noted that for 4dd7 , these three Cl atoms were mis-interpreted first of all by us (ST and JRH), with evidence of their presence coming from all four processing programs.

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 ) and ( d ) 4dd9 processed by XDS and EVAL and ( e ) and ( f ) 4g4c processed by XDS and EVAL , respectively.

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 .

The largest transformation took place in 4dd7 , a crystal with only three days of storage.

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 ▶ ).

The F o − F c OMIT electron-density maps are shown in green and the anomalous difference electron-density maps are shown in orange at a 3σ cutoff: 4dd7 (Tanley, Diederichs et al. , 2013 a ▶ ) processed by ( a ) XDS (Kabsch, 2010 ▶ ) and ( b ) EVAL (Schreurs et al. , 2010 ▶ ).

Publication Year: 2014