Table 2. X-ray Diffraction Data Collection and Refinement of Tetragonal Structuresa.
apo | NAD+ | |
---|---|---|
beamline | APS 19-ID-C | ALS 4.2.2 |
space group | P4212 | P4212 |
unit cell parameters | a = 159.3 Å | a = 158.9 Å |
c = 79.8 Å | c = 79.4 Å | |
wavelength | 0.979 | 1.000 |
resolution (Å) | 46.0–1.90 (1.93–1.90) | 53.0–1.90 (1.94–1.90) |
no. of observations | 1175993 | 1175225 |
no. of unique reflections | 81138 | 80249 |
Rmerge(I) | 0.097 (1.209) | 0.102 (1.445) |
Rmeas(I) | 0.100 (1.256) | 0.105 (1.504) |
Rpim(I) | 0.026 (0.336) | 0.028 (0.411) |
mean I/σ | 20.9 (2.4) | 23.7 (2.5) |
mean CC1/2 | 0.999 (0.743) | 0.999 (0.697) |
completeness (%) | 99.8 (96.5) | 99.7 (95.0) |
multiplicity | 14.5 (13.5) | 14.6 (13.3) |
no. of protein chains | 2 | 2 |
no. of protein residues | 948 | 946 |
no. of protein atoms | 7076 | 6994 |
no. of NAD+ atoms | – | 23 |
no. of water molecules | 312 | 385 |
Rcryst | 0.169 (0.281) | 0.182 (0.269) |
Rfreeb | 0.195 (0.329) | 0.213 (0.305) |
rmsd for bond lengths (Å) | 0.007 | 0.007 |
rmsd for bond angles (deg) | 0.973 | 0.967 |
Ramachandran plotc (%) | ||
favored | 98.30 | 98.51 |
outliers | 0.11 | 0.00 |
all-atom Clashscorec | 1.3 | 2.2 |
average B factor (Å2) | ||
protein | 34.8 | 35.2 |
NAD+ | – | 35.1 |
water | 35.0 | 32.8 |
coordinate error (Å)d | 0.19 | 0.20 |
PDB entry | 4ZVX | 4ZVY |
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.