5QK7
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z1918536193
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) | 0.91587 |
Spacegroup name | P 1 |
Unit cell lengths | 48.577, 59.461, 80.404 |
Unit cell angles | 79.39, 82.31, 76.19 |
Refinement procedure
Resolution | 78.680 - 1.660 |
R-factor | 0.2186 |
Rwork | 0.217 |
R-free | 0.25490 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 6gru |
RMSD bond length | 0.016 |
RMSD bond angle | 1.768 |
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] | 46.960 | 46.960 | 1.750 |
High resolution limit [Å] | 1.660 | 5.260 | 1.660 |
Rmerge | 0.036 | 0.025 | 1.245 |
Rmeas | 0.051 | 0.035 | 1.761 |
Rpim | 0.036 | 0.025 | 1.245 |
Total number of observations | 155480 | 5172 | 23708 |
Number of reflections | 88015 | ||
<I/σ(I)> | 7.5 | 22.3 | 0.5 |
Completeness [%] | 87.7 | 92.1 | 94.8 |
Redundancy | 1.8 | 1.8 | 1.7 |
CC(1/2) | 0.998 | 0.997 | 0.389 |
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 |