8P5R
Crystal structure of full-length, homohexameric 2-oxoglutarate dehydrogenase KGD from Mycobacterium smegmatis in complex with GarA
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | SOLEIL BEAMLINE PROXIMA 1 |
| Synchrotron site | SOLEIL |
| Beamline | PROXIMA 1 |
| Temperature [K] | 100 |
| Detector technology | CCD |
| Collection date | 2008-11-21 |
| Detector | ADSC QUANTUM 315r |
| Wavelength(s) | 0.9763 |
| Spacegroup name | P 65 |
| Unit cell lengths | 325.750, 325.750, 396.944 |
| Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
| Resolution | 45.990 - 4.562 |
| R-factor | 0.1998 |
| Rwork | 0.198 |
| R-free | 0.22920 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.006 |
| RMSD bond angle | 0.730 |
| Data reduction software | autoPROC |
| Data scaling software | Aimless (0.7.7) |
| Phasing software | PHASER |
| Refinement software | BUSTER (2.10.4 (8-JUN-2022)) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 282.108 | 282.108 | 4.778 |
| High resolution limit [Å] | 4.562 | 12.910 | 4.562 |
| Rmerge | 0.245 | 0.054 | 1.915 |
| Rmeas | 0.257 | 0.057 | 2.001 |
| Rpim | 0.076 | 0.017 | 0.583 |
| Total number of observations | 1388278 | 65721 | 71365 |
| Number of reflections | 121219 | 6059 | 6059 |
| <I/σ(I)> | 8.11 | 28.08 | 1.48 |
| Completeness [%] | 94.6 | 99.9 | 52.9 |
| Completeness (spherical) [%] | 89.6 | 99.9 | 34.8 |
| Completeness (ellipsoidal) [%] | 94.6 | 99.9 | 52.9 |
| Redundancy | 11.45 | 10.85 | 11.78 |
| CC(1/2) | 0.998 | 0.999 | 0.701 |
| Anomalous completeness (spherical) | 89.7 | 99.7 | 35.0 |
| Anomalous completeness | 94.6 | 99.7 | 53.0 |
| Anomalous redundancy | 5.8 | 5.6 | 5.9 |
| CC(ano) | -0.117 | -0.255 | -0.034 |
| |DANO|/σ(DANO) | 0.7 | 0.5 | 0.7 |
| Diffraction limits | Principal axes of ellipsoid fitted to diffraction cut-off surface |
| 4.713 Å | 1.000, 1.000, 1.000 |
| 4.713 Å | 0.000, 0.000, 0.000 |
| 4.562 Å | 0.000, 0.000, 0.000 |
| 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 | 291 | 0.1 M bicine pH 8.0, 30% (v/v) PEG550MME, 0.2 M NaCl |
