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. Author manuscript; available in PMC: 2010 Apr 6.
Published in final edited form as: Structure. 2008 Dec 10;16(12):1849–1859. doi: 10.1016/j.str.2008.10.010

Table 2.

Data collection and refinement statistics

WT E1p (Mn-ThDP) S1-E1p (Mg-ThDP) Phospho-S1-E1p (apo) Phospho-S1-E1p (Mn-ThDP) Y89F-α E1p (apo)e
PDB code 3EXE 3EXF 3EXG 3EXH 3EXI
Data collectiona
Space group P21 P21 P1 C2 P3221
No. of E1p heterotetramers in the asymmetric unit 2 2 8 2 0.5 (one heterodimer)
Unit cell
a (Å) 103.57 103.39 119.28 154.38 257.06
b (Å) 129.62 129.67 128.29 154.38 115.61
c (Å) 124.30 144.95 228.41 82.95 127.59
α (°) 90 90 90.14 90 90
β (°) 92.48 109.16 90.05 90 113.64
γ (°) 90 90 90.02 120 90
Wavelength (Å) 0.98 0.98 0.98 1.54 (Cu-Kα) 0.98
Resolution (Å) 1.98 3.0 3.0 2.45 2.20
Unique reflections 225065 72201 263005 123888 57582
Completeness (%) 99.6 (99.0) 99.8 (98.2) 98.4 (98.0) 98.1 (96.6) 99.5 (99.5)
R-merge (%)b 10.7 (55.1) 14.6 (56.0) 8.0 (53.5) 15.5 (69.3) 3.4 (39.9)
<I>/<σ(I)> 13.3 (2.3) 10.7 (2.6) 10.3 (1.7) 14.2 (2.8) 33.0 (2.0)
Multiplicity 4.9 (4.8) 3.7 (3.4) 2.1 (1.9) 6.7 (6.5) 6.6 (6.5)
Refinementa
No. reflections (Work/Test) 213690/11272 68497/3624 249289/13221 117572/6182 55098/1511
No. atoms (Mean B value (Å2))
 Protein 21379 (17.7) 21386 (21.6) 83323 (55.7) 5106 (49.2) 21081 (18.8)
 Solvents 2316 (26.5) 9 (6.9) 0 318 (51.0) 792 (19.0)
 ThDP 104 (11.4) 104 (25.4) 0 0 104 (17.7)
 Metal and other 32 (32.4) 8 (32.8) 16 (75.3) 3 (65.7) 58 (41.3)
R-work (%)c 15.8 (20.1) 18.4 (23.9) 18.9 (29.5) 16.5 (23.4) 18.7 (28.1)
R-free (%)c 20.6 (26.9) 26.2 (35.8) 25.3 (37.4) 21.0 (28.5) 22.5 (34.8)
R.m.s.d
 Bond length (Å) 0.021 0.021 0.019 0.020 0.020
 Bond angle (°) 1.761 2.044 1.883 1.733 1.842
Ramachandran plot
 Most favored (%) 96.5 90.2 92.1 96.1 96.3
 Allowed (%) 2.2 6.8 5.7 2.8 2.5
 Disallowed (%) 1.3 3.0 d 2.2 d 1.1 1.2
a

Values in parentheses refer to data in the highest resolution shell unless otherwise indicated.

b

R-merge = Σhkl Σj | Ij - <I> | / Σhkl Σj Ij, where <I> is the mean intensity of j observations from a reflection hkl and its symmetry equivalents.

c

R-work = Σhkl| |Fobs| − k|Fcalc| | / Σhkl |Fobs|. R-free = R-work for 5 % of reflections that were omitted from refinement.

d

The higher numbers result from the lower resolution (3.0 Å) of these structures than the others.

e

This crystal contains a complex of Y89F-α E1p with SBD, but SBD is not visible and excluded from the model.

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