4WEQ | pdb_00004weq

Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc02828 (SmGhrA) from Sinorhizobium meliloti in complex with NADP and sulfate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		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, 0.5 mM TCEP, and 5 mM NADP were mixed with 0.2 ul of the MCSG-I condition #6 (0.2 M Ammonium Sulfate 0.1 M Bis-Tris:HCl pH 5.5 25% (w/v) PEG 3350) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization, the protein-ligand mixture was incubated with 1/40 v/v of 2 mg/ml chymotrypsin solution at 289 K for 3 hours

Crystal Properties
Matthews coefficient	Solvent content
3.92	68.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.153	α = 90
b = 108.153	β = 90
c = 80.657	γ = 120

Symmetry
Space Group	P 32 2 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	ADSC QUANTUM 315r		2014-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97912	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	0.069	0.072	0.021	9.4	12.2		37017		-3	38.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge 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		0.846	0.883	0.252	0.92		12.2	1828

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2	50	35220	1769	99.92	0.1561	0.1543	0.17	0.1962	0.2	RANDOM	48.923

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]
0.87	0.44		0.87		-2.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.203
r_dihedral_angle_4_deg	16.206
r_dihedral_angle_3_deg	12.187
r_dihedral_angle_1_deg	5.759
r_mcangle_it	2.542
r_mcbond_it	1.887
r_mcbond_other	1.887
r_angle_refined_deg	1.754
r_angle_other_deg	0.84
r_chiral_restr	0.099

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.203
r_dihedral_angle_4_deg	16.206
r_dihedral_angle_3_deg	12.187
r_dihedral_angle_1_deg	5.759
r_mcangle_it	2.542
r_mcbond_it	1.887
r_mcbond_other	1.887
r_angle_refined_deg	1.754
r_angle_other_deg	0.84
r_chiral_restr	0.099
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.006
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2415
Nucleic Acid Atoms
Solvent Atoms	250
Heterogen Atoms	77

Software

Software
Software Name	Purpose
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
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.