5V72

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5UOG	PDB entry 5UOG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	289	0.2 uL of 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 + 0.2 uL MCSG Suite II condition #9 (0.1 M sodium citrate, pH 5.0, 20% w/v PEG6000), equilibrated against 1.5 M sodium chloride in a 96-well 3-drop crystallization plate (Swissci), incubated with 1/50 v/v 2 mg/mL chymotrypsin solution at 289 K for 3 hours prior to crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.188	α = 90
b = 157.926	β = 110.74
c = 64.719	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD	Beryllium Lenses	2014-07-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.1	50	98.4	0.096	0.096	0.115	0.062	6.7	3.2		68211		-3	28

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.14	99.1		0.431	0.431	0.515	0.279	0.834	2.3	3.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 5UOG	2.1	50	64518	3350	98.36	0.1662	0.1642	0.204	RANDOM	35.344

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.95		-1.07	2.13		-1.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.347
r_dihedral_angle_4_deg	22.175
r_dihedral_angle_3_deg	12.873
r_dihedral_angle_1_deg	5.904
r_angle_refined_deg	1.464
r_angle_other_deg	0.978
r_chiral_restr	0.082
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.347
r_dihedral_angle_4_deg	22.175
r_dihedral_angle_3_deg	12.873
r_dihedral_angle_1_deg	5.904
r_angle_refined_deg	1.464
r_angle_other_deg	0.978
r_chiral_restr	0.082
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9315
Nucleic Acid Atoms
Solvent Atoms	1151
Heterogen Atoms	28

Software

Software
Software Name	Purpose
MD2	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.