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Table 2 Data statistics for crystals C1 - C7.

From: New insight into the dynamic properties and the active site architecture of H-Ras p21 revealed by X-ray crystallography at very high resolution

 

Crystal name and nucleotide content

 

C1 GppNHp

C2 GDP

C3 S-caged GTP

C4 R-caged GTP

C5 R-caged GTP→GTP

C6 R-caged GTP→GDP

C7 R-caged GTP→GTP

Data collection and processing

Synchrotron (Beamline)

ESRF (ID14-1)

SLS (PX-I)

ESRF (ID14-4)

ESRF (ID14-4)

ESRF (ID14-4)

ESRF (ID14-4)

ESRF (ID14-4)

Area detector

Q4R ADSC

CCD CHESS

Q4R ADSC

Q4R ADSC

Q4R ADSC

Q4R ADSC

Q4R ADSC

Temperature (K)

100

100

100

100

100

100

100

Wavelength (Å)

0.934

0.827

0.920

0.939

0.976

0.939

0.976

Space group

R32

C222(1)

P4(1)

P4(1)

P4(1)

P4(1)

P4(1)

Cell dimensions (Å)

a = b = 88.5 c = 144.1

a = 49.0 b = 53.8 c = 116.0

a = b = 69.1 c = 35.5

a = b = 69.1 c = 35.5

a = b = 69.3 c = 35.0

a = b = 69.4 c = 34.8

a = b = 69.3 c = 35.0

Resolution limit a (Å)

67.42 - 1.70 (1.75 - 1.70)

50.00 - 0.99 (1.00 - 0.99)

69.01 - 1.24 (1.26 - 1.24)

69.34 - 1.00 (1.05 - 1.00)

69.34 - 1.25 (1.30 - 1.25)

69.34 - 1.22 (1.30 - 1.22)

69.34 - 1.30 (1.40 - 1.30)

Number of recorded reflections

276701

400222

317470

541277

283084

286285

258379

Number of unique recorded reflections

23933

82821

46194

91096

46204

47013

41195

Average redundancy

11.6

4.8

6.9

5.9

6.1

6.1

6.3

R sym a,b (%)

8.1 (86.1)

4.9 (60.5)

4.9 (33.4)

5.2 (67.9)

4.3 (51.5)

4.6 (45.7)

5.5 (54.9)

Average I/σ a (I)

16.9 (2.1)

15.0 (2.3)

18.7 (3.1)

13.6 (2.3)

20.7 (3.5)

21.5 (3.0)

16.05 (3.14)

B -factor from Wilson plot (Å 2 )

30.9

12.0

18.3

14.0

21.1

22.1

22.6

Refinement statistics

Resolution range a (Å)

67.42 - 1.80 (1.85 - 1.80)

50.00 - 1.00 (1.03 - 1.00)

69.01 - 1.24 (1.27 - 1.24)

69.34 - 1.05 (1.08 - 1.05)

69.34 - 1.25 (1.28 - 1.25)

69.34 - 1.22 (1.25 - 1.22)

69.34 - 1.30 (1.33 - 1.30)

Number of unique reflections

19368

76394

44152

78796

43911

44702

39138

Completeness of data a (%)

99.88 (100.00)

96.95 (96.03)

96.78 (76.25)

99.93 (99.97)

99.92 (99.94)

94.12 (55.47)

100.00 (100.00)

R work a,c / R free a,d (%)

14.6/18.5 (18.9/23.7)

14.4/16.3 (27.0/27.7)

14.6/18.6 (21.8/21.2)

15.6/18.1 (26.5/27.9)

14.8/17.0 (24.6/24.3)

14.9/17.6 31.4/34.5

14.9/18.0 (27.2/30.9)

Ramachandran plot e Favored, allowed, generous, disallowed (%)

94.7, 5.3, 0.0, 0.0

89.3, 10.0, 0.7, 0.0

87.3, 10.3, 1.0, 0.3

89.3, 9.0, 1.0, 0.7

90.0, 9.7, 0.0, 0.3

90.0, 9.0, 0.7, 0.3

89.7, 10.0, 0.0, 0.3

Rmsd on bond lengths (Å)

0.016

0.012

0.012

0.015

0.015

0.011

0.015

Rmsd on bond angles (deg)

1.808

1.719

1.625

1.855

1.742

1.534

1.753

Mean B -factors (Å 2 )

       

   Backbone (conformation A|B)

30.0

8.0 | 8.4

14.2 | 14.9

5.2 | 4.8

7.0 | 8.5

18.0 | 16.6

13.0 | 14.9

   Side-chain (conformation A|B)

34.4

10.3 | 11.0

16.1 | 17.2

7.4 | 6.9

10.1 | 11.3

20.58 | 18.3

15.9 | 17.7

   Nucleotide (conformation A|B)

25.7

6.8 | 6.8

15.0 | 16.2

6.0 | 7.3

6.7 | 7.2

20.0 | 16.0

12.3 | 12.6

   Fluorophore (conformation A|B)

85.6

32.0 | 33.4

23.6 | 30.8

19.7 | 12.5

42.0 | 32.2

-

43.5 | 42.4

   Solvent

49.4

24.0

26.3

28.5

29.7

38.2

24.1

PDB ID

2CL0

2CE2

2CL6

2EVW

2CL7

2CLD

2CLC

  1. a Values in parentheses are for the high-resolution bin.
  2. b R s y m = 100 × h i | I i ( h ) I i ( h ) | / h i I i ( h ) , where I i (h) is the i th measurement and Ii(h) is the mean of all measurements of I(h) for Miller indices hkl.
  3. c R = ( | | F o b s | k | F c a l c | | ) / | F o b s | , where F obs and F calc are observed and calculated structure factor amplitudes, respectively.
  4. d R free value is the R value obtained for a test set of reflections, consisting of a randomly selected 5% subset of the diffraction data not used during refinement [36].
  5. e Calculated using the program PROCHECK [37].