3GRK

Crystal structure of short chain dehydrogenase reductase SDR glucose-ribitol dehydrogenase from Brucella melitensis

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	PACT Premier screen condition C11, 20% PEG 6000, 0.2 M CaCl2, 0.1 M HEPES NaOH pH 7.0, 47.3 mg/mL protein, crystal ID 200296c11, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.1	α = 90
b = 120.1	β = 99.2
c = 137.7	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	RIGAKU SATURN 944		2008-10-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.35	20	95.1	0.074	14.3			84019		-3	37.157

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.35	2.41	79.1		0.364	3.6		5125

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.35	19.81	84017	4211	95.27	0.209	0.206	0.269	RANDOM	27.873

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]
0.21		0.04	-0.34		0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.445
r_dihedral_angle_4_deg	16.09
r_dihedral_angle_3_deg	15.019
r_dihedral_angle_1_deg	5.711
r_scangle_it	2.247
r_scbond_it	1.333
r_angle_refined_deg	1.113
r_mcangle_it	1.028
r_angle_other_deg	0.816
r_mcbond_it	0.543

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.445
r_dihedral_angle_4_deg	16.09
r_dihedral_angle_3_deg	15.019
r_dihedral_angle_1_deg	5.711
r_scangle_it	2.247
r_scbond_it	1.333
r_angle_refined_deg	1.113
r_mcangle_it	1.028
r_angle_other_deg	0.816
r_mcbond_it	0.543
r_mcbond_other	0.081
r_chiral_restr	0.061
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15116
Nucleic Acid Atoms
Solvent Atoms	563
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.