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Table 3 Crystallographic data processing and refinement statistics

From: Molecular insights into substrate recognition and catalytic mechanism of the chaperone and FKBP peptidyl-prolyl isomerase SlyD

  TtSlyDFL:T1 TtSlyDFL:S2 TtSlyDFL:S2-W23A TtSlyDFL:S2-plus TtSlyDFL:FK506 TtSlyD∆IF:S2-W23A TtSlyD∆IF:S3 TtSlyD∆IF:FK506
Data collection
 Beamline Diamond
I24
Diamond
I03
Diamond
I02
Diamond
I04-1
Diamond
I24
Diamond
I24
SOLEIL
Proxima 1
SOLEIL
Proxima 1
 Wavelength (Å) 0.9191 0.9795 0.9199 0.9200 1.0000 1.4000 1.0332 0.9801
 Space group C2 P6222 C2 P21 P1 P4132 P4132 P43212
 Cell dimensions
   a, b, c (Å) 87.50
52.99
48.91
110.88
110.88
182.31
184.12
41.20
131.52
39.83
40.55
53.22
48.71
50.21
57.67
93.69
93.69
93.69
93.56
93.56
93.56
72.50
72.50
178.96
  α, β, γ (°) 90
111.18
90
90
90
120
90
123.13
90
90
91.24
90
85.74
68.92
80.12
90
90
90
90
90
90
90
90
90
 Resolution (Å) 29.10–1.40
(1.44–1.40)
48.01–2.92
(2.99–2.92)
29.11–1.75
(1.80–1.75)
28.41–1.60
(1.64–1.60)
27.81–1.60
(1.64–1.60)
29.63–1.75
(1.79–1.75)
38.20–2.00
(2.05–2.00)
44.48–1.93
(1.98–1.93)
R sym 0.023 (0.714) 0.047 (0.679) 0.047 (0.766) 0.097 (0.772) 0.052 (0.568) 0.044 (0.872) 0.106 (0.774) 0.048 (0.777)
I/σI 23.03 (2.02) 30.68 (3.27) 18.31 (2.42) 12.74 (2.29) 14.46 (2.47) 35.85 (3.60) 23.33 (4.38) 26.27 (2.75)
 Completeness (%) 97.6 (93.7) 99.1 (99.8) 98.9 (97.6) 99.3 (97.7) 95.3 (87.4) 100 (99.9) 100 (100) 99.9 (99.5)
 Total number of reflections 134,551 (9,116) 126,159 (9,085) 307,806 (22,441) 151,369 (9,923) 219,115 (13,672) 475,595 (32,633) 417,094 (29,168) 523,651 (36,435)
 Multiplicity 3.3 (3.2) 8.4 (8.5) 3.7 (3.7) 6.7 (6.1) 3.5 (3.2) 17.6 (16.4) 23.3 (22.1) 7.6 (7.2)
 Wilson B-factor (Å) 23.11 84.82 26.98 15.67 20.93 29.88 26.17 32.03
Refinement
R work / R free 0.139 / 0.167 0.210 / 0.224 0.176 / 0.208 0.177 / 0.198 0.180 / 0.202 0.184 / 0.202 0.199 / 0.215 0.156 / 0.168
 Number of TtSlyD/ASU 1 2 4 1 3 1 1 2
 Number of atoms
  Protein 1,229 2,314 4,708 1,179 3,558 814 843 1,650
  Peptides/FK506 102 469 705 105 171 43 49 114
  Water 195 6 606 228 630 100 107 316
  Other solvent 1 2 20 30 27 6 6 53
B-factors
  Protein 30.1 71.2 32.4 15.6 29.4 41.1 29.1 31.0
  Peptides/FK506 36.0 88.9 45.7 33.7 28.6 78.7 45.5 32.2
  Solvent 45.4 41.6 42.3 34.6 39.1 46.0 35.8 50.2
 R.m.s. deviations
  Bond lengths (Å) 0.005 0.003 0.006 0.017 0.004 0.016 0.009 0.014
  Angles (°) 1.027 0.759 1.094 1.177 0.947 1.258 0.839 1.100
 Ramachandran
  Favored (%) 99.4 95.0 98.5 98.8 98.7 100 97.2 98.1
  Outliers (%) 0.0 0.3 0.0 0.0 0.0 0.0 0.0 0.0
 Clash score 1.9 2.0 2.2 4.7 4.3 2.4 2.9 4.7
 PDB accession 4ODK 4ODL 4ODM 4ODN 4ODO 4ODP 4ODQ 4ODR
  1. All three TtSlyD∆IF data sets were processed anomalously, while the full-length TtSlyD data sets were not. Numbers in parentheses refer to statistics for the outer shell. The Ramachandran statistics and clash scores were determined using the MolProbity validation tool