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PDB ID Mentions in PubMed Central Article count: 2

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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

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 , ... dd6 , 4dd7 , 4dd9 , 4dda , 4ddb , 4ddc (from Tanley et al. , 2012 ▶ )].

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.

Crystal 1 2 3 PDB code 3txb 4dd0   3txd 4dd2   3txe 4dd3   Software d*Trek EVAL Mosflm d*Trek EVAL Mosflm d*Trek EVAL Mosflm Unit cell † a = 78.66 a = 78.69 a = 78.61 a = 78.88 a = 78.91 a = 78.90 a = 78.66 a = 78.53 a = 78.54   c = 36.96 c = 36.90 c = 36.91 c = 36.99 c = 36.99 c = 37.00 c = 37.44 c = 37.36 c = 37.38 Observed reflections 416806 336926 390544 366668 271407 267042 248915 239297 243139 Unique reflections 17504 13312 14988 16526 14462 10457 13378 13144 12223 Resolution () 55.621.59 (1.641.59) 19.671.70 (1.761.70) 18.771.63 (1.731.63) 55.771.53 (1.591.53) 19.731.55 (1.601.55) 26.991.78 (1.871.78) 55.511.70 (1.761.70) 31.011.70 (1.761.70) 17.711.75 (1.841.75) Completeness (%) 99.3 (93.2) 99.9 (100) 99.9 (100) 91.4 (38.4) 82.6 ‡ (53.0) 88.4 (100) 98.0 (82.3) 98.1 (82.9) 99.5 (95.8) R merge 0.106 (0.377) 0.104 (0.64) 0.106 (1.36) 0.076 (0.327) 0.063 (0.456) 0.071 (0.24) 0.084 (0.395) 0.062 (0.314) 0.067 (0.30) Merged mean I / 20.9 (8.4) 22.7 (4.4) 20.1 (2.2) 21.1 (2.1) 30.3 (2.1) 33.2 (11.1) 14.7 (4.2) 32.6 (7.3) 32.0 (8.9) Redundancy 25.8 (18.9) 25.3 (25.8) 26.1 (24.6) 11.9 (2.5) 18.8 (4.2) 25.5 (24.8) 18.9 (14.0) 18.3 (13.2) 19.9 (18.3) B Wilson 15.2 17.4 23.8 25.5 22.1 20.6 22.5 18.9 18.0 Average atomic B factor () 31.4 18.5 29.9 35.2 23.0 23.3 31.0 17.8 18.9 R factor/ R free (%) 20.9/25.6 18.7/23.6 17.7/22.8 19.8/25.9 20.0/24.5 18.9/25.1 20.0/25.8 19.2/23.6 18.9/25.0 R factor (all) 20.9 18.9 18.0 20.6 20.2 19.2 21.6 19.4 19.2 R.m.s.d. bond lengths ()/angles () 0.0359/2.4021 0.017/1.924 0.0192/1.8505 0.0259/2.0605 0.0187/2.0721 0.0188/1.8168 0.0241/1.9858 0.0191/1.9181 0.0195/1.8769 Crystal 4 10 11 PDB code 3txi 4dd9   3txj 4dda   3txk 4ddb Software d*Trek EVAL Mosflm d*Trek EVAL Mosflm d*Trek EVAL Unit cell † a = 78.66 a = 78.53 a = 78.04 a = 78.53 a = 78.37 a = 78.48 a = 79.46 a = 79.64   c = 36.98 c = 37.36 c = 37.98 c = 36.72 c = 36.58 c = 36.99 c = 36.96 c = 37.02 Observed reflections 358383 296297 310742 56396 49543 61525 13178 79530 Unique reflections 15336 15451 11554 4343 4120 4991 4150 3234 Resolution () 55.181.60 (1.661.60) 31.011.70 (1.761.70) 26.841.78 (1.881.78) 55.532.48 (2.572.48) 19.592.40 (2.482.40) 25.462.38 (2.512.38) 56.193.00 (3.113.00) 30.942.50 (2.582.50) Completeness (%) 98.8 (90.5) 98.9 (89.7) 100 (100) 99.2 (93.1) 85.3 ‡ (100) 99.9 (100) 91.3 ‡ (91.9) 72 (100) R merge 0.053 (0.220) 0.047 (0.154) 0.051 (0.13) 0.199 (0.412) 0.147 (0.607) 0.226 (0.87) 0.15 (0.266) 0.136 (0.528) Merged mean I / 36.4 (6.2) 42.8 (6.6) 50.0 (22.7) 9.4 (4.8) 13.6 (4.0) 7.8 (2.5) 5.8 (3.2) 27.8 (6.3) Redundancy 23.7 (7.4) 19.2 (4.5) 26.9 (25.8) 12.9 (11.5) 12.1 (12.8) 12.3 (12.7) 3.18 (3.15) 24.6 (24.5) B Wilson 22.2 18.9 20.3 34.0 35.2 37.0 48.0 34.9 Average atomic B factor () 29.9 18.6 23.1 32.3 29.9 48.4 42.1 17.8 R factor/ R free (%) 18.7/23.3 18.3/22.3 18.9/23.9 22.3/28.9 20.0/28.5 21.2/26.6 21.1/25.8 21.4/27.9 R factor (all) 19.1 18.5 19.2 22.5 20.4 21.4 20.2 21.6 R.m.s.d. bond lengths ()/angles () 0.0280/2.3712 0.0200/2.0684 0.0199/2.0314 0.0219/1.94328 0.0126/2.3771 0.0186/1.6260 0.0217/2.0624 0.007/1.173 Processing with Mosflm did not succeed.

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

Table 1 Anomalous difference density peak heights ( cut-off level) in the N and N binding sites for Cl atoms for three different datasets using a number of different processing programs   �... 0a0; Anomalous peak height     N Cl N Cl1 N Cl2 HEWL co-crystallized with carboplatin in 10% NaCl and DMSO media with glycerol as the cryoprotectant 3txh PROTEUM2 4.4 4.7 4.4 MOSFLM 3.6 4.8 4.2 4dd7_ EVAL 3.6 3.6 3.6 XDS 3.9 4.0 3.8 HEWL co-crystallized with carboplatin in 10% NaCl and DMSO media with paratone as the cryoprotectant 3txi d*TREK 0 0 0 MOSFLM 2.5 4.2 2.2 4dd9_ EVAL 3.0 3.8 0 XDS 2.8 4.1 2.4 HEWL co-crystallized with carboplatin in 10% NaCl and DMSO media studied at room temperature 4g4c_ EVAL 2.4 2.5 2.8 PROTEUM2 0 0 0 XDS 0 3.1 0 Table 2 Correlation coefficient of cisplatin or carboplatin binding in the 2 F o F c map for both the N and N atoms of His-15 using OVERLAPMAP in CCP4i , with the Pt centre removed, i.e the calculation is just for the remaining bound ligands Note that in this calculation each ligand is considered separately whereas in the SHELX calculation summarized in Table 3 ▶ both of the ligand occupancies are refined in the same calculation.

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