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. 2015 Aug 11;54(35):5513–5522. doi: 10.1021/acs.biochem.5b00754

Table 1. X-ray Diffraction Data Collection and Refinement of Monoclinic Structuresa.

  AA NAD+ apo
beamline APS 19-ID-C ALS 4.2.2 APS 24-ID-E
space group C2 C2 C2
unit cell parameters a = 154.4 Å a = 155.7 Å a = 157.0 Å
  b =  162.5 Å b =  161.6 Å b =  162.5 Å
  c =  158.7 Å c =  158.9 Å c =  160.0 Å
  β = 95.0° β = 94.8° β = 94.1°
wavelength 0.979 1.000 0.979
resolution (Å) 47.9–1.76 (1.79–1.76) 62.9–2.00 (2.03–2.00) 16.0–2.40 (2.44–2.40)
no. of observations 1405606 995590 559499
no. of unique reflections 381768 261450 153212
Rmerge(I) 0.066 (0.657) 0.106 (1.050) 0.150 (0.313)
Rmeas(I) 0.078 (0.773) 0.123 (1.224) 0.176 (0.370)
Rpim(I) 0.040 (0.404) 0.063 (0.626) 0.063 (0.626)
mean I 12.3 (1.9) 12.7 (1.3) 6.3 (3.1)
mean CC1/2 0.998 (0.682) 0.997 (0.632) 0.967 (0.874)
completeness (%) 99.4 (99.8) 99.5 (96.1) 98.2 (99.7)
multiplicity 3.7 (3.6) 3.8 (3.7) 3.7 (3.5)
no. of protein chains 8 8 8
no. of protein residues 4070 4062 4056
no. of protein atoms 30562 30440 29450
no. of AA atoms 88
no. of NAD+ atoms 200
no. of water molecules 1899 1345 557
Rcryst 0.168 (0.261) 0.171 (0.288) 0.226 (0.243)
Rfreeb 0.206 (0.308) 0.218 (0.352) 0.275 (0.312)
rmsd for bond lengths (Å) 0.006 0.007 0.003
rmsd for bond angles (deg) 1.000 1.021 0.738
Ramachandran plotc (%)      
favored 96.97 96.91 96.93
outliers 0.25 0.20 0.02
all-atom Clashscorec 2.1 2.5 2.3
average B factor (Å2)      
protein 24.5 30.0 37.4
AA 31.3
NAD+ 40.0
water 29.3 29.7 28.4
coordinate error (Å)d 0.20 0.24 0.36
PDB entry 4ZUL 4ZUK 4ZVW
a

Values for the outer resolution shell of data are given in parentheses.

b

The 5% test set.

c

Generated with MolProbity via PHENIX refine.

d

Maximum likelihood-based coordinate error estimate reported by PHENIX refine.