7YUZ
Human K-Ras G12D (GDP-bound) in complex with cyclic peptide inhibitor AP8784
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | SLS BEAMLINE X10SA |
| Synchrotron site | SLS |
| Beamline | X10SA |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2021-09-04 |
| Detector | DECTRIS EIGER X 16M |
| Wavelength(s) | 1.000006 |
| Spacegroup name | P 31 2 1 |
| Unit cell lengths | 66.012, 66.012, 86.330 |
| Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
| Resolution | 34.450 - 1.878 |
| R-factor | 0.2611 |
| Rwork | 0.259 |
| R-free | 0.29850 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.008 |
| RMSD bond angle | 0.930 |
| Data reduction software | XDS (Jan 31, 2020) |
| Data scaling software | Aimless (0.7.7) |
| Phasing software | PHASER |
| Refinement software | BUSTER (2.11.8 (20-APR-2021)) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 34.450 | 34.448 | 2.079 |
| High resolution limit [Å] | 1.878 | 5.978 | 1.878 |
| Rmerge | 0.051 | 0.034 | 1.830 |
| Rmeas | 0.052 | 0.035 | 1.884 |
| Rpim | 0.012 | 0.008 | 0.442 |
| Total number of observations | 10494 | 11481 | |
| Number of reflections | 12671 | 634 | 636 |
| <I/σ(I)> | 23.58 | 66.96 | 1.53 |
| Completeness [%] | 94.0 | 100 | 69.1 |
| Completeness (spherical) [%] | 100.0 | 13.5 | |
| Completeness (ellipsoidal) [%] | 100.0 | 69.1 | |
| Redundancy | 19.28 | 16.55 | 18.05 |
| CC(1/2) | 0.999 | 0.999 | 0.664 |
| Anomalous completeness (spherical) | 100.0 | 12.3 | |
| Anomalous completeness | 100.0 | 69.3 | |
| Anomalous redundancy | 10.0 | 9.9 | |
| CC(ano) | 0.220 | -0.021 | |
| |DANO|/σ(DANO) | 1.4 | 0.6 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.2 M Ammonium iodide, 20.0 %w/v Polyethylene glycol 3,350, and 25%v/v Ethylene glycol as a cryoprotectant |
