5UNN

Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc02828 (SmGhrA) from Sinorhizobium meliloti in apo form

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4Z0P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	289	0.2 ul of 12 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG suite I condition # 88 (0.1 M Sodium citrate pH=5.6, 20% v/v 2-Propanol, 20% w/v PEG 4000 ) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci)

Crystal Properties
Matthews coefficient	Solvent content
3.66	66.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.592	α = 90
b = 128.592	β = 90
c = 122.847	γ = 90

Symmetry
Space Group	I 41

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	2015-04-18	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	50	100	0.108	0.108	0.117	0.044	6.9	6.9		67353		-3	28.5

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	2.03	100		0.902	0.902	0.986	0.389	0.615	1.7	6.6

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	4Z0P	2	50	63691	3517	99.86	0.1482	0.1468	0.1742	RANDOM	44.268

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]
-0.19			-0.19		0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.372
r_dihedral_angle_4_deg	19.916
r_dihedral_angle_3_deg	11.181
r_dihedral_angle_1_deg	5.6
r_angle_refined_deg	1.369
r_angle_other_deg	0.927
r_chiral_restr	0.083
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.372
r_dihedral_angle_4_deg	19.916
r_dihedral_angle_3_deg	11.181
r_dihedral_angle_1_deg	5.6
r_angle_refined_deg	1.369
r_angle_other_deg	0.927
r_chiral_restr	0.083
r_bond_refined_d	0.011
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	3424
Nucleic Acid Atoms
Solvent Atoms	659
Heterogen Atoms	13

Software

Software
Software Name	Purpose
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
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.