5QK0
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z1270312110
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 | 2018-07-28 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.91587 |
Spacegroup name | P 1 |
Unit cell lengths | 49.672, 60.151, 79.779 |
Unit cell angles | 79.37, 80.65, 75.23 |
Refinement procedure
Resolution | 77.830 - 1.440 |
R-factor | 0.3077 |
Rwork | 0.306 |
R-free | 0.33840 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 6gru |
RMSD bond length | 0.006 |
RMSD bond angle | 0.972 |
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] | 47.680 | 47.680 | 1.520 |
High resolution limit [Å] | 1.440 | 4.550 | 1.440 |
Rmerge | 0.041 | 0.038 | 1.119 |
Rmeas | 0.058 | 0.054 | 1.583 |
Rpim | 0.041 | 0.038 | 1.119 |
Total number of observations | 216147 | 7740 | 21832 |
Number of reflections | 130398 | ||
<I/σ(I)> | 6.3 | 21.1 | 0.4 |
Completeness [%] | 82.5 | 85.9 | 70 |
Redundancy | 1.7 | 1.8 | 1.4 |
CC(1/2) | 0.995 | 0.992 | 0.464 |
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 |