24HS
Human KRAS G12D (GDP-bound) in complex with macrocyclic peptide inhibitor AP4959
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 21 21 21 |
| Unit cell lengths | 111.254, 112.810, 202.783 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 101.390 - 2.530 |
| R-factor | 0.2299 |
| Rwork | 0.227 |
| R-free | 0.28970 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Data reduction software | XDS (Jan 31, 2020) |
| Data scaling software | Aimless (0.7.15) |
| 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] | 101.392 | 101.392 | 2.829 |
| High resolution limit [Å] | 2.526 | 8.042 | 2.526 |
| Rmerge | 0.311 | 0.086 | 3.101 |
| Rmeas | 0.344 | 0.095 | 3.429 |
| Rpim | 0.145 | 0.040 | 1.442 |
| Total number of observations | 323803 | 15461 | 15950 |
| Number of reflections | 57707 | 2885 | 2885 |
| <I/σ(I)> | 6.46 | 14.11 | 1.67 |
| Completeness [%] | 87.4 | 99.9 | 38.7 |
| Completeness (spherical) [%] | 66.9 | 99.9 | 11.7 |
| Completeness (ellipsoidal) [%] | 87.4 | 99.9 | 38.7 |
| Redundancy | 5.61 | 5.36 | 5.53 |
| CC(1/2) | 0.980 | 0.995 | 0.443 |
| Anomalous completeness (spherical) | 65.6 | 99.8 | 11.5 |
| Anomalous completeness | 86.5 | 99.8 | 39.4 |
| Anomalous redundancy | 3.0 | 3.1 | 2.9 |
| CC(ano) | -0.060 | -0.304 | -0.008 |
| |DANO|/σ(DANO) | 0.7 | 0.5 | 0.8 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | 60.0% v/v Tacsimate |
