5RY4
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z300245038
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 | 2019-10-24 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.91589 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 62.470, 79.150, 89.350 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 59.250 - 1.470 |
R-factor | 0.1744 |
Rwork | 0.173 |
R-free | 0.19800 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 6xy7 |
RMSD bond length | 0.009 |
RMSD bond angle | 1.572 |
Data reduction software | XDS |
Data scaling software | Aimless (0.7.4) |
Phasing software | REFMAC |
Refinement software | REFMAC (5.8.0238) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 79.150 | 79.150 | 1.510 |
High resolution limit [Å] | 1.470 | 6.570 | 1.470 |
Rmerge | 0.125 | 0.047 | 1.530 |
Rmeas | 0.136 | 0.051 | 1.699 |
Rpim | 0.053 | 0.020 | 0.728 |
Total number of observations | 483531 | 5925 | 29482 |
Number of reflections | 75851 | ||
<I/σ(I)> | 8.7 | 28.9 | 1 |
Completeness [%] | 99.8 | 99.8 | 99.6 |
Redundancy | 6.4 | 6.1 | 5.3 |
CC(1/2) | 0.997 | 0.998 | 0.445 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM MES/imidazole, pH 6.5, 20% PEG500 MME, 10% PEG20000 |