8WB1
Crystal Structure of small molecule KN2H covalently bound to K-Ras(G12D)
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SSRF BEAMLINE BL19U1 |
Synchrotron site | SSRF |
Beamline | BL19U1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2023-06-10 |
Detector | DECTRIS PILATUS3 6M |
Wavelength(s) | 0.97852 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 40.099, 51.955, 90.475 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 25.980 - 1.720 |
R-factor | 0.1934 |
Rwork | 0.192 |
R-free | 0.21150 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.009 |
RMSD bond angle | 1.204 |
Data reduction software | HKL-3000 |
Data scaling software | HKL-3000 |
Phasing software | PHASER |
Refinement software | PHENIX ((1.20.1_4487)) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 1.780 |
High resolution limit [Å] | 1.720 | 3.710 | 1.720 |
Rmerge | 0.115 | 0.090 | 0.561 |
Rmeas | 0.121 | 0.094 | 0.593 |
Rpim | 0.036 | 0.028 | 0.191 |
Total number of observations | 251226 | ||
Number of reflections | 21135 | 2276 | 2048 |
<I/σ(I)> | 7.2 | ||
Completeness [%] | 99.8 | 99.7 | 98.7 |
Redundancy | 11.9 | 11 | 9.3 |
CC(1/2) | 0.995 | 0.995 | 0.895 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 289 | 0.06M citric acid, 0.04M bis-tris propane, pH 4.1, 16% w/v peg3350 |