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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 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.

The result is that for crystals 2 ( 4dd2 ), 10 ( 4dda ), 11 ( 4ddb ), 6 ( 4dd4 ) and 7 ( 4dd6 ) the completeness (Tables 2 ▶ and 3 ▶ ) dropped to 82–91%.

Data sets 10 ( 4dda ) and 11 ( 4ddb ) are exceptions because of the low resolution and concomitant TLS refinement only.

The changes in R merge were insignificant, whereas the protein model refinement R / R free values were only noticeably different for the lower-resolution crystals: R / R free = 21.4/29.9 versus 20.0/28.5 (de-iced) for crystal 10 ( 4dda ) and 28.5/34.8 versus 21.4/27.9 for de-iced for crystal 11 ( 4ddb ).

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 .

EVAL ’s diffraction data processing statistics in Tables 2 ▶ and 3 ▶ show that the quality of the crystals varies somewhat, but mostly they diffract to approximately 1.7 Å, except for two crystals ( 4dda and 4ddb ), which simply did not diffract further than 2.4–2.5 Å.

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 .

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