9R3L
Structure of liver pyruvate kinase in complex with fluorescent probe 4d
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 | 2023-03-14 |
| Detector | DECTRIS EIGER2 X 16M |
| Wavelength(s) | 0.95374 |
| Spacegroup name | P 1 |
| Unit cell lengths | 110.880, 111.312, 118.978 |
| Unit cell angles | 103.60, 104.13, 118.12 |
Refinement procedure
| Resolution | 105.260 - 2.158 |
| R-factor | 0.2408 |
| Rwork | 0.239 |
| R-free | 0.27300 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.008 |
| RMSD bond angle | 0.910 |
| 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] | 105.263 | 105.263 | 2.520 |
| High resolution limit [Å] | 2.158 | 7.849 | 2.158 |
| Rmerge | 0.120 | 0.051 | 0.864 |
| Rmeas | 0.140 | 0.060 | 1.010 |
| Rpim | 0.073 | 0.031 | 0.520 |
| Total number of observations | 350390 | 18729 | 18179 |
| Number of reflections | 96839 | 4842 | 4842 |
| <I/σ(I)> | 6.05 | 14.23 | 1.85 |
| Completeness [%] | 86.4 | 97.5 | 68.1 |
| Completeness (spherical) [%] | 40.6 | 97.5 | 5.5 |
| Completeness (ellipsoidal) [%] | 86.4 | 97.5 | 68.1 |
| Redundancy | 3.62 | 3.87 | 3.75 |
| CC(1/2) | 0.989 | 0.989 | 0.610 |
| Anomalous completeness (spherical) | 39.3 | 94.1 | 5.4 |
| Anomalous completeness | 83.6 | 94.1 | 67.6 |
| Anomalous redundancy | 1.9 | 2.0 | 1.9 |
| CC(ano) | -0.167 | -0.140 | 0.007 |
| |DANO|/σ(DANO) | 0.8 | 0.5 | 0.8 |
| Diffraction limits | Principal axes of ellipsoid fitted to diffraction cut-off surface |
| 2.158 Å | 0.771, 0.771, 0.771 |
| 2.926 Å | -0.117, -0.117, -0.117 |
| 3.414 Å | 0.626, 0.626, 0.626 |
| 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 |
