6PEJ

Structure of sorbitol dehydrogenase from Sinorhizobium meliloti 1021 bound to sorbitol

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	50 mM sodium acetate, 100 mM HEPES pH 7.4, 18% PEG 3000, 20% sorbitol

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.298	α = 90
b = 88.298	β = 117.39
c = 87.317	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	93	IMAGE PLATE	RIGAKU RAXIS IV++		2017-04-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5419

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	39.6	98	0.139	5.4	3		74395

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)
1	2	10			0.522

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	6PEI	2	39.08	70800	3581	97.92	0.1968	0.1941	0.2494	RANDOM	19.442

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]
0.99		-1.58	-0.01		0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.743
r_dihedral_angle_4_deg	19.488
r_dihedral_angle_3_deg	16.796
r_dihedral_angle_1_deg	7.256
r_mcangle_it	2.581
r_angle_other_deg	2.469
r_angle_refined_deg	1.927
r_mcbond_it	1.848
r_mcbond_other	1.848
r_chiral_restr	0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.743
r_dihedral_angle_4_deg	19.488
r_dihedral_angle_3_deg	16.796
r_dihedral_angle_1_deg	7.256
r_mcangle_it	2.581
r_angle_other_deg	2.469
r_angle_refined_deg	1.927
r_mcbond_it	1.848
r_mcbond_other	1.848
r_chiral_restr	0.1
r_bond_other_d	0.037
r_bond_refined_d	0.015
r_gen_planes_other	0.015
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7588
Nucleic Acid Atoms
Solvent Atoms	905
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing

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 R01GM133198.