7R4K
Crystal structure of human mitochondrial NAD kinase
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ESRF BEAMLINE ID30B |
Synchrotron site | ESRF |
Beamline | ID30B |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2021-09-13 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.9763 |
Spacegroup name | P 43 21 2 |
Unit cell lengths | 67.583, 67.583, 221.815 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 37.090 - 3.330 |
R-factor | 0.2173 |
Rwork | 0.214 |
R-free | 0.28680 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | alphafold |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHASER |
Refinement software | PHENIX (1.19.1-4122) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 37.090 | 37.090 | 3.160 |
High resolution limit [Å] | 2.980 | 8.780 | 2.980 |
Rmerge | 0.276 | 0.088 | 2.379 |
Rmeas | 0.319 | 0.102 | 2.750 |
Rpim | 0.153 | 0.671 | |
Number of reflections | 18108 | 697 | 2832 |
<I/σ(I)> | 2.94 | 13.31 | |
Completeness [%] | 89.0 | 87.1 | 87.1 |
Redundancy | 3.379 | 3.605 | 3.126 |
CC(1/2) | 0.962 | 0.987 | 0.200 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | PEG 400 28% v/v, CaCl2 150 mM, 0.1 M Sodium HEPES, 2% glycerol |