4MIO

Crystal Structure of myo-inositol dehydrogenase from Lactobacillus casei in complex with NAD(H) and myo-inositol

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	6.5	298	ammonium sulfate, pH 6.5, MICROBATCH, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.693	α = 90
b = 110.48	β = 90
c = 126.738	γ = 90

Symmetry
Space Group	P 21 21 21

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	RAYONIX MX300HE		2011-07-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08B1-1	0.97949	CLSI	08B1-1

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	1.5	83.28	100	0.062	16.8	7	238638	238638	-3	-3	17.05

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	1.5	1.58	100		0.797	0.797	0.9	6.2	34572

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	1.5	48.865	1.35	238638	238508	11962	99.98	0.1809	0.1798	0.2007	RANDOM	20.9784

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.14
f_angle_d	1.338
f_chiral_restr	0.118
f_bond_d	0.025
f_plane_restr	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10488
Nucleic Acid Atoms
Solvent Atoms	1166
Heterogen Atoms	308

Software

Software
Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MxDC	data collection
XDS	data reduction

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.