7YV1
Human K-Ras G12D (GDP-bound) in complex with cyclic peptide inhibitor LUNA18 and KA30L Fab
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | SPRING-8 BEAMLINE BL45XU |
| Synchrotron site | SPring-8 |
| Beamline | BL45XU |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2020-10-07 |
| Detector | DECTRIS PILATUS 6M |
| Wavelength(s) | 1.00000 |
| Spacegroup name | P 21 21 21 |
| Unit cell lengths | 65.617, 90.373, 116.810 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 58.410 - 1.454 |
| R-factor | 0.2397 |
| Rwork | 0.238 |
| R-free | 0.27720 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 7VO2 |
| RMSD bond length | 0.008 |
| RMSD bond angle | 1.010 |
| Data reduction software | XDS (Jan 26, 2018) |
| Data scaling software | Aimless (0.7.4) |
| Phasing software | PHASER |
| Refinement software | BUSTER (2.11.8 (20-APR-2021)) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 58.410 | 58.405 | 1.535 |
| High resolution limit [Å] | 1.454 | 4.347 | 1.454 |
| Rmerge | 0.134 | 0.052 | 1.284 |
| Rmeas | 0.141 | 0.054 | 1.455 |
| Rpim | 0.044 | 0.017 | 0.654 |
| Total number of observations | 51363 | 22414 | |
| Number of reflections | 97915 | 4895 | 4897 |
| <I/σ(I)> | 16.42 | 43.73 | 1.55 |
| Completeness [%] | 90.3 | 99.9 | 51.2 |
| Redundancy | 9.35 | 10.49 | 4.58 |
| CC(1/2) | 0.997 | 0.998 | 0.227 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 293 | 2.0 %v/v Tacsimate (pH 5.0), 0.1 M tri-Sodium citrate (pH 5.6), 16.0 %w/v Polyethylene glycol 3,350, and 25 %v/v Ethylene glycerol as a cryoprotectant |
