5QKB
Ground-state model of NUDT5 and corresponding apo datasets for PanDDA analysis
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I04-1 |
Synchrotron site | Diamond |
Beamline | I04-1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2018-07-29 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 1.000 |
Spacegroup name | P 1 |
Unit cell lengths | 49.074, 59.679, 80.321 |
Unit cell angles | 79.44, 81.82, 75.93 |
Refinement procedure
Resolution | 78.540 - 1.580 |
R-factor | 0.221 |
Rwork | 0.219 |
R-free | 0.25000 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 6gru |
RMSD bond length | 0.019 |
RMSD bond angle | 1.997 |
Data reduction software | XDS |
Data scaling software | Aimless (0.7.1) |
Phasing software | REFMAC |
Refinement software | REFMAC (5.8.0189) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 47.320 | 47.320 | 1.620 |
High resolution limit [Å] | 1.580 | 7.070 | 1.580 |
Rmerge | 0.032 | 0.025 | 0.338 |
Rmeas | 0.045 | 0.035 | 0.478 |
Rpim | 0.032 | 0.025 | 0.338 |
Total number of observations | 193270 | 2330 | 11879 |
Number of reflections | 113271 | ||
<I/σ(I)> | 9.8 | 27 | 1.1 |
Completeness [%] | 95.6 | 97.4 | 93.1 |
Redundancy | 1.7 | 1.8 | 1.5 |
CC(1/2) | 0.997 | 0.996 | 0.813 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 293.15 | 33 % PEG4k, 0.2 MgCl2 and 0.1 M Tris |