5V6Q

Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc04462 (SmGhrB) from Sinorhizobium meliloti in complex with NADP and malonate

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 21-ID-G
Synchrotron site	APS
Beamline	21-ID-G
Temperature [K]	100
Detector technology	CCD
Collection date	2014-07-24
Detector	MARMOSAIC 300 mm CCD
Wavelength(s)	0.97856
Spacegroup name	H 3
Unit cell lengths	176.484, 176.484, 135.857
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	40.290 - 1.950
R-factor	0.1444
Rwork	0.144
R-free	0.15650
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	5j23
RMSD bond length	0.009
RMSD bond angle	1.340
Data reduction software	HKL-3000
Data scaling software	HKL-3000
Phasing software	MOLREP
Refinement software	REFMAC (5.8.0135)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	50.000	50.000	1.980
High resolution limit [Å]	1.950	5.290	1.950
Rmerge	0.105	0.057	0.691
Rmeas	0.119	0.065	0.784
Rpim	0.055	0.030	0.366
Number of reflections	114355		5653
<I/σ(I)>	7.6		2.1
Completeness [%]	99.6	99.5	98.6
Redundancy	4.6	4.4	4.5
CC(1/2)		0.996	0.686

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	7	289	0.2 uL 13 mg/mL protein in 20 mM HEPES, pH 7.5, 150 mM sodium chloride, 10% glycerol, 0.1% sodium azide, 0.5 mM TCEP, 5 mM NADP + 0.2 uL MCSG Suite II condition #20 (1.1 M malonic acid, 0.072 M succinic acid, 0.15 M ammonium citrate tribasic, 0.18 M DL-malic acid, 0.096 M ammonium tartrate dibasic, 0.24 M sodium acetate, 0.3 M sodium formate, pH 7), equilibrated against 1.5 M sodium chloride in a 96-well, 3-drop crystallization plate (Swissci), incubated with 1/50 v/v 1 mg/mL rTEV at 289 K for 3 hours prior to crystallization