9R3O
Structure of liver pyruvate kinase in complex with fluorescent probe 4a
This is a non-PDB format compatible entry.
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | DIAMOND BEAMLINE I04 |
| Synchrotron site | Diamond |
| Beamline | I04 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2023-01-26 |
| Detector | DECTRIS EIGER2 X 16M |
| Wavelength(s) | 0.95374 |
| Spacegroup name | C 1 2 1 |
| Unit cell lengths | 206.883, 112.002, 188.129 |
| Unit cell angles | 90.00, 91.90, 90.00 |
Refinement procedure
| Resolution | 188.030 - 2.045 |
| R-factor | 0.2074 |
| Rwork | 0.206 |
| R-free | 0.23960 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.008 |
| RMSD bond angle | 0.920 |
| Data reduction software | XDS (Jan 10, 2022) |
| Data scaling software | Aimless (0.7.9) |
| Phasing software | PHASER |
| Refinement software | BUSTER (2.10.4) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 103.384 | 103.384 | 2.280 |
| High resolution limit [Å] | 2.045 | 6.615 | 2.045 |
| Rmerge | 0.183 | 0.060 | 1.663 |
| Rmeas | 0.198 | 0.065 | 1.789 |
| Rpim | 0.074 | 0.024 | 0.654 |
| Total number of observations | 1158706 | 60055 | 61566 |
| Number of reflections | 164483 | 8224 | 8224 |
| <I/σ(I)> | 7.04 | 17.82 | 1.5 |
| Completeness [%] | 90.1 | 100 | 64.3 |
| Completeness (spherical) [%] | 60.9 | 100.0 | 11.0 |
| Completeness (ellipsoidal) [%] | 90.1 | 100.0 | 64.3 |
| Redundancy | 7.04 | 7.3 | 7.49 |
| CC(1/2) | 0.995 | 0.998 | 0.998 |
| Anomalous completeness (spherical) | 60.1 | 99.7 | 11.0 |
| Anomalous completeness | 89.2 | 99.7 | 65.3 |
| Anomalous redundancy | 3.6 | 3.8 | 3.8 |
| CC(ano) | -0.236 | -0.565 | -0.044 |
| |DANO|/σ(DANO) | 0.7 | 0.5 | 0.8 |
| Diffraction limits | Principal axes of ellipsoid fitted to diffraction cut-off surface |
| 2.725 Å | 0.757, 0.757, 0.757 |
| 2.316 Å | 0.000, 0.000, 0.000 |
| 2.043 Å | -0.654, -0.654, -0.654 |
| Criteria used in determination of diffraction limits | local <I/sigmaI> ≥ 1.2 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 291 | 100 mM HEPES/MOPS, 10% PEG8000, 20% ethylene glycol, 10 mM phenylalanine, 20 mM sodium oxalate |
