9R3I
Structure of liver pyruvate kinase in complex with fluorescent probe 4c
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 | C 1 2 1 |
| Unit cell lengths | 190.121, 113.026, 140.304 |
| Unit cell angles | 90.00, 132.05, 90.00 |
Refinement procedure
| Resolution | 28.320 - 2.579 |
| R-factor | 0.2434 |
| Rwork | 0.241 |
| R-free | 0.29140 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.007 |
| RMSD bond angle | 0.880 |
| 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] | 104.191 | 104.191 | 2.973 |
| High resolution limit [Å] | 2.579 | 8.813 | 2.579 |
| Rmerge | 0.244 | 0.064 | 1.336 |
| Rmeas | 0.263 | 0.069 | 1.450 |
| Rpim | 0.098 | 0.026 | 0.559 |
| Total number of observations | 260538 | 12806 | 11947 |
| Number of reflections | 36371 | 1819 | 1819 |
| <I/σ(I)> | 5.68 | 14.03 | 1.53 |
| Completeness [%] | 92.5 | 99.9 | 68 |
| Completeness (spherical) [%] | 52.3 | 99.9 | 7.6 |
| Completeness (ellipsoidal) [%] | 92.5 | 99.9 | 68.0 |
| Redundancy | 7.16 | 7.04 | 6.57 |
| CC(1/2) | 0.993 | 0.996 | 0.556 |
| Anomalous completeness (spherical) | 51.8 | 99.7 | 7.4 |
| Anomalous completeness | 92.5 | 99.7 | 68.6 |
| Anomalous redundancy | 3.7 | 3.7 | 3.4 |
| CC(ano) | -0.147 | -0.433 | -0.039 |
| |DANO|/σ(DANO) | 0.7 | 0.3 | 0.8 |
| Diffraction limits | Principal axes of ellipsoid fitted to diffraction cut-off surface |
| 2.563 Å | 0.762, 0.762, 0.762 |
| 3.373 Å | 0.000, 0.000, 0.000 |
| 3.545 Å | -0.647, -0.647, -0.647 |
| 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 |
