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/σ | 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 |
Values for the outer resolution shell of data are given in parentheses.
The 5% test set.
Generated with MolProbity via PHENIX refine.
Maximum likelihood-based coordinate error estimate reported by PHENIX refine.