Experiment: 3MZ0

Crystal structure of apo myo-inositol dehydrogenase from Bacillus subtilis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		low resolution SeMet-IDH model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	7.5	277	0.2M MgCl2, 0.1M HEPES pH 7.5, 30% PEG 400, microbatch, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.207	α = 90
b = 120.054	β = 90
c = 129.254	γ = 90

Symmetry
Space Group	I 2 2 2

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 225 mm CCD		2007-08-17	M	SAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97961	CLSI	08ID-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	1.539	19.7	99.4	0.076	0.076	16.2	6.9		60036			21.5

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)
	1.539	1.6	99.9		0.231	0.231	7.7	6.2	5943

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	low resolution SeMet-IDH model	1.539	19.696	1.34	1.34	60036	60009	3066	99.22	0.1759	0.1749	0.1716	0.1935	0.1915	RANDOM	21.5

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]
5.2019			-0.0188		-5.1831

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.808
f_angle_d	1.101
f_chiral_restr	0.078
f_bond_d	0.006
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2640
Nucleic Acid Atoms
Solvent Atoms	375
Heterogen Atoms	31

Software

Software
Software Name	Purpose
HKL-2000	data collection
SHARP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling