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