3CEA

Crystal structure of myo-inositol 2-dehydrogenase (NP_786804.1) from Lactobacillus plantarum at 2.40 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	NANODROP, 0.2M MgCl2, 20.0% PEG 1000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.331	α = 90
b = 145.684	β = 91.92
c = 100.208	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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2007-12-10	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97941, 0.97883	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.4	29.45	99	0.133	0.133	9.3	3.6		52411			33.924

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.46	91.8		0.429	0.429	1.9	2	3467

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	MAD	THROUGHOUT	2.4	29.45	52383	2662	99.02	0.196	0.193	0.243	RANDOM	45.891

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]
4.46		-0.01	-2.35		-2.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.841
r_dihedral_angle_3_deg	13.561
r_dihedral_angle_4_deg	12.6
r_dihedral_angle_1_deg	4.653
r_scangle_it	1.987
r_scbond_it	1.317
r_angle_refined_deg	0.934
r_mcangle_it	0.752
r_mcbond_it	0.409
r_nbtor_refined	0.292

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.841
r_dihedral_angle_3_deg	13.561
r_dihedral_angle_4_deg	12.6
r_dihedral_angle_1_deg	4.653
r_scangle_it	1.987
r_scbond_it	1.317
r_angle_refined_deg	0.934
r_mcangle_it	0.752
r_mcbond_it	0.409
r_nbtor_refined	0.292
r_nbd_refined	0.168
r_xyhbond_nbd_refined	0.101
r_symmetry_vdw_refined	0.1
r_chiral_restr	0.057
r_symmetry_hbond_refined	0.046
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10435
Nucleic Acid Atoms
Solvent Atoms	343
Heterogen Atoms	189

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXD	phasing
SHARP	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.