9NZM
Crystal Structure of Kirsten Rat Sarcoma G12C Complexed with GMPPNP and Covalently Bound to an Adduct of {(2S)-4-[7-(8-chloronaphthalen-1-yl)-2-{[(2S)-1-methylpyrrolidin-2-yl]methoxy}-5,6,7,8-tetrahydropyrido[3,4-d]pyrimidin-4-yl]-1-[(2Z)-2-fluoro-3-(pyridin-2-yl)prop-2-enoyl]piperazin-2-yl}acetonitrile
This is a non-PDB format compatible entry.
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | APS BEAMLINE 17-ID |
| Synchrotron site | APS |
| Beamline | 17-ID |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2021-10-07 |
| Detector | DECTRIS EIGER X 9M |
| Wavelength(s) | 1.00000 |
| Spacegroup name | C 1 2 1 |
| Unit cell lengths | 111.788, 70.420, 62.783 |
| Unit cell angles | 90.00, 111.07, 90.00 |
Refinement procedure
| Resolution | 18.140 - 1.586 |
| R-factor | 0.2103 |
| Rwork | 0.209 |
| R-free | 0.22930 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.010 |
| RMSD bond angle | 0.990 |
| Data reduction software | XDS (Jan 10, 2022) |
| Data scaling software | Aimless (0.7.15) |
| Phasing software | PHASER |
| Refinement software | BUSTER (2.11.8) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 58.587 | 58.587 | 1.740 |
| High resolution limit [Å] | 1.586 | 4.962 | 1.586 |
| Rmerge | 0.107 | 0.047 | 1.549 |
| Rmeas | 0.119 | 0.052 | 1.683 |
| Rpim | 0.050 | 0.022 | 0.651 |
| Total number of observations | 221095 | 11072 | 12940 |
| Number of reflections | 41310 | 2066 | 2065 |
| <I/σ(I)> | 8.38 | 20.5 | 1.5 |
| Completeness [%] | 90.7 | 99.3 | 54.6 |
| Completeness (spherical) [%] | 67.1 | 99.3 | 13.9 |
| Completeness (ellipsoidal) [%] | 90.7 | 99.3 | 54.6 |
| Redundancy | 5.35 | 5.36 | 6.27 |
| CC(1/2) | 0.996 | 0.997 | 0.540 |
| Anomalous completeness (spherical) | 65.8 | 99.0 | 13.1 |
| Anomalous completeness | 89.9 | 99.0 | 54.4 |
| Anomalous redundancy | 2.7 | 2.8 | 3.3 |
| CC(ano) | -0.316 | -0.383 | -0.005 |
| |DANO|/σ(DANO) | 0.7 | 0.5 | 0.7 |
| Diffraction limits | Principal axes of ellipsoid fitted to diffraction cut-off surface |
| 1.611 Å | 0.766, 0.766, 0.766 |
| 2.072 Å | 0.000, 0.000, 0.000 |
| 1.628 Å | 0.643, 0.643, 0.643 |
| Criteria used in determination of diffraction limits | local <I/sigmaI> ≥ 1.2 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 277 | 100 MM Sodium cacodylate, pH 6.5, 1 M tri-sodium citrate dihydrate |
