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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