8QHQ
Crystal structure of human DNPH1 bound to hmdUMP
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I03 |
Synchrotron site | Diamond |
Beamline | I03 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2021-04-23 |
Detector | DECTRIS EIGER2 XE 16M |
Wavelength(s) | 0.9763 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 56.648, 67.126, 120.117 |
Unit cell angles | 90.00, 99.63, 90.00 |
Refinement procedure
Resolution | 55.850 - 1.780 |
R-factor | 0.2066 |
Rwork | 0.206 |
R-free | 0.22440 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.002 |
RMSD bond angle | 0.560 |
Data reduction software | XDS (Feb 5, 2021) |
Data scaling software | pointless (1.12.8) |
Phasing software | PHASER (2.8.3) |
Refinement software | PHENIX (1.20.1_4487) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 59.212 | 1.806 |
High resolution limit [Å] | 1.775 | 1.775 |
Rmerge | 0.125 | |
Rmeas | 0.132 | |
Rpim | 0.042 | |
Number of reflections | 80370 | 3316 |
<I/σ(I)> | 11.7 | |
Completeness [%] | 93.5 | |
Redundancy | 9.5 | |
CC(1/2) | 0.999 | 0.398 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 0.2 M sodium fluoride, 0.1 M Bis-Tris propane pH 6.5, 20% w/v PEG 3350 |