24HR
Human KRAS G12D (GDP-bound) in complex with macrocyclic peptide inhibitor AP6252
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 43 21 2 |
| Unit cell lengths | 111.480, 111.480, 201.402 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 62.070 - 2.070 |
| R-factor | 0.2301 |
| Rwork | 0.228 |
| R-free | 0.27010 |
| 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] | 97.535 | 97.535 | 2.304 |
| High resolution limit [Å] | 2.069 | 6.931 | 2.069 |
| Rmerge | 0.154 | 0.052 | 2.061 |
| Rmeas | 0.159 | 0.054 | 2.131 |
| Rpim | 0.037 | 0.013 | 0.534 |
| Total number of observations | 839548 | 41030 | 35352 |
| Number of reflections | 46355 | 2318 | 2318 |
| <I/σ(I)> | 14.29 | 41.64 | 1.69 |
| Completeness [%] | 93.2 | 100 | 71.1 |
| Completeness (spherical) [%] | 59.4 | 100.0 | 10.9 |
| Completeness (ellipsoidal) [%] | 93.2 | 100.0 | 71.1 |
| Redundancy | 18.11 | 17.7 | 15.25 |
| CC(1/2) | 0.999 | 0.999 | 0.714 |
| Anomalous completeness (spherical) | 57.6 | 100.0 | 9.9 |
| Anomalous completeness | 92.6 | 100.0 | 69.0 |
| Anomalous redundancy | 9.7 | 10.6 | 8.3 |
| CC(ano) | -0.035 | -0.030 | -0.017 |
| |DANO|/σ(DANO) | 0.7 | 0.7 | 0.7 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 293 | 4.0M Sodium formate |
