4HKT | pdb_00004hkt

Crystal structure of a putative myo-inositol dehydrogenase from Sinorhizobium meliloti 1021 (Target PSI-012312)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	298	Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol, Reservoir (MCSG1 #93; H9: 0.1 M Bis-Tris:HCl pH 5.5, 25% (w/v) PEG 3350 ), Cryoprotection (30% Ethylene glycol), VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.449	α = 90
b = 55.467	β = 97.56
c = 149.091	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	ADSC QUANTUM 315	MIRRORS	2012-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.97910	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	2	50	99.8	0.086	16.87	6.2		99392			24.8

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	2	2.03	97.3		0.528	3.64	6.1	4809

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	SAD	THROUGHOUT	2	41	99374	4995	99.62	0.188	0.1857	0.1995	0.2317	0.1984	RANDOM	35.4543

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]
1.85		-0.06	-0.08		-1.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.6
r_dihedral_angle_4_deg	19.137
r_dihedral_angle_3_deg	13.571
r_dihedral_angle_1_deg	5.802
r_angle_refined_deg	1.401
r_angle_other_deg	0.759
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	37.6
r_dihedral_angle_4_deg	19.137
r_dihedral_angle_3_deg	13.571
r_dihedral_angle_1_deg	5.802
r_angle_refined_deg	1.401
r_angle_other_deg	0.759
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	9852
Nucleic Acid Atoms
Solvent Atoms	632
Heterogen Atoms	120

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-3000	data reduction
SCALEPACK	data scaling
SHELX	phasing
SHELXD	phasing
SHELXE	model building

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.