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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

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 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.

Indexing of all diffraction data was straightforward with DIRAX (Duisenberg, 1992 ▶ ), except for 4dd1 and 4ddc (see later).

† Space group is P 4 3 2 1 2 for all data except for EVAL data 4dd1 and 4ddc , where it is P 2 1 2 1 2 1 .

For example, crystals 5 ( 4dd1 ) and 9 ( 4ddc ) have significantly higher refined B factors with PROTEUM and Mosflm data processing, because loss of tetragonal symmetry was not recognized (see below), in our hands (JRH and ST), and therefore the difference in conformation between the two independent molecules was modelled as a type of static disorder.

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 9 ( 4ddc ), when indexed with 4/ mmm symmetry, gave positional errors on the detector of 0.18 mm (corresponding to more than 2 pixels) and a 0.14° error in rotation angle, far too large in our view.

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 .

Figure 10 Distribution of horizontal (in units of 0.01 mm) and rotational (in units of 0.01°) peak shifts of data 4ddc in EVAL15 .

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

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