5QK6
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z1343633025
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 | 49.260, 59.800, 80.310 |
Unit cell angles | 79.26, 81.50, 75.67 |
Refinement procedure
Resolution | 78.450 - 1.510 |
R-factor | 0.2282 |
Rwork | 0.227 |
R-free | 0.25490 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 6gru |
RMSD bond length | 0.017 |
RMSD bond angle | 1.877 |
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] | 41.430 | 41.430 | 1.550 |
High resolution limit [Å] | 1.510 | 6.750 | 1.510 |
Rmerge | 0.069 | 0.062 | 0.682 |
Rmeas | 0.097 | 0.087 | 0.964 |
Rpim | 0.069 | 0.062 | 0.681 |
Total number of observations | 223045 | 2709 | 13175 |
Number of reflections | 130552 | ||
<I/σ(I)> | 8.6 | 21.4 | 1 |
Completeness [%] | 95.8 | 98.2 | 93.6 |
Redundancy | 1.7 | 1.8 | 1.4 |
CC(1/2) | 0.982 | 0.973 | 0.511 |
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 |