5QJD
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z240297434
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 | 2018-07-07 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.91587 |
Spacegroup name | P 1 |
Unit cell lengths | 48.728, 59.593, 80.188 |
Unit cell angles | 79.65, 82.00, 76.23 |
Refinement procedure
Resolution | 78.480 - 1.610 |
R-factor | 0.2113 |
Rwork | 0.210 |
R-free | 0.23690 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 6gru |
RMSD bond length | 0.011 |
RMSD bond angle | 1.569 |
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] | 78.500 | 78.500 | 1.650 |
High resolution limit [Å] | 1.610 | 7.200 | 1.610 |
Rmerge | 0.033 | 0.022 | 0.595 |
Rmeas | 0.047 | 0.031 | 0.841 |
Rpim | 0.033 | 0.022 | 0.595 |
Total number of observations | 179910 | 2215 | 11312 |
Number of reflections | 105862 | ||
<I/σ(I)> | 9.8 | 29.8 | 0.8 |
Completeness [%] | 95.3 | 98.6 | 92.8 |
Redundancy | 1.7 | 1.8 | 1.5 |
CC(1/2) | 0.994 | 0.996 | 0.672 |
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 |