24HT
Human KRAS G12D (GDP-bound) in complex with macrocyclic peptide inhibitor AP2527
This is a non-PDB format compatible entry.
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 | 2025-01-22 |
| Detector | DECTRIS EIGER X 16M |
| Wavelength(s) | 0.99999 |
| Spacegroup name | P 61 |
| Unit cell lengths | 66.476, 66.476, 86.805 |
| Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
| Resolution | 57.570 - 1.700 |
| R-factor | 0.1972 |
| Rwork | 0.195 |
| R-free | 0.23930 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 7yv1 |
| Data reduction software | XDS (Jan 31, 2020) |
| Data scaling software | STARANISO (2.4.16) |
| Phasing software | PHASER (2.8.3) |
| Refinement software | PHENIX (1.21.2_5419) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 57.570 | 57.570 | 1.910 |
| High resolution limit [Å] | 1.700 | 5.169 | 1.701 |
| Rmerge | 0.197 | 0.047 | 3.232 |
| Rmeas | 0.203 | 0.049 | 3.340 |
| Rpim | 0.048 | 0.011 | 0.837 |
| Total number of observations | 15843 | 13565 | |
| Number of reflections | 17465 | 873 | 873 |
| <I/σ(I)> | 9.09 | 24.24 | 1.48 |
| Completeness [%] | 94.4 | 100 | 53.9 |
| Completeness (spherical) [%] | 100.0 | 12.5 | |
| Completeness (ellipsoidal) [%] | 100.0 | 53.9 | |
| Redundancy | 17.75 | 18.15 | 15.54 |
| CC(1/2) | 0.999 | 0.999 | 0.557 |
| Anomalous completeness (spherical) | 100.0 | 12.8 | |
| Anomalous completeness | 100.0 | 53.9 | |
| Anomalous redundancy | 9.5 | 7.8 | |
| CC(ano) | 0.277 | -0.070 | |
| |DANO|/σ(DANO) | 0.5 | 0.8 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 293 | 0.1M Sodium acetate trihydrate (pH 4.6), 8.0 %w/v Polyethylene glycol 4000 |
