4EJ6

Crystal structure of a putative zinc-binding dehydrogenase (Target PSI-012003) from Sinorhizobium meliloti 1021

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.2	298	Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (MCSG1 #3: 0.2 M Sodium Chloride 0.1 M Na2HPO4:KH2PO4 10% (w/v) PEG 8000 ); Cryoprotection (30% Ethylene glycol), temperature 298K, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.607	α = 90
b = 107.607	β = 90
c = 137.16	γ = 90

Symmetry
Space Group	I 4 2 2

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 315	MIRRORS	2011-10-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.9791	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	1.89	50	99.8	0.083	33.7	23	32173	32173			30.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.93	99.9		0.8	5.4	20.6	1560

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.89	50	32166	1627	99.7	0.1774	0.1761	0.2018	RANDOM	36.4674

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]
-1.24			-1.24		2.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.194
r_dihedral_angle_4_deg	22.218
r_dihedral_angle_3_deg	11.034
r_dihedral_angle_1_deg	6.171
r_angle_refined_deg	1.332
r_angle_other_deg	0.89
r_chiral_restr	0.079
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.194
r_dihedral_angle_4_deg	22.218
r_dihedral_angle_3_deg	11.034
r_dihedral_angle_1_deg	6.171
r_angle_refined_deg	1.332
r_angle_other_deg	0.89
r_chiral_restr	0.079
r_bond_refined_d	0.009
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	2492
Nucleic Acid Atoms
Solvent Atoms	185
Heterogen Atoms	70

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SHELX	phasing
SHELXD	phasing
SHELXE	model building

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.