7D5N

Crystal structure of inositol dehydrogenase homolog complexed with NADH and myo-inositol from Azotobacter vinelandii

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DTY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.2 M Ca acetate, 14% PEG3350,10 mM NADH, 50 mM myo-inositol

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.81	α = 90
b = 151.53	β = 90
c = 48.12	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	CCD	ADSC QUANTUM 315		2011-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.980	Photon Factory	BL-17A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.8	50	92.5	0.064	0.999	19.9	6.9		63455

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.85	59.7		0.558	0.788	2.5	5.3

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3DTY	1.8	48.166	63455	3177	92.482	0.18	0.1794	0.19	0.1969	0.2	22.52

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]
0.458			-0.964		0.506

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.58
r_dihedral_angle_4_deg	20.047
r_dihedral_angle_3_deg	12.244
r_dihedral_angle_1_deg	6.897
r_lrange_it	4.326
r_lrange_other	4.324
r_scangle_it	3.452
r_scangle_other	3.451
r_mcangle_it	2.145
r_mcangle_other	2.145
r_scbond_it	2.144
r_scbond_other	2.144
r_angle_other_deg	1.499
r_mcbond_it	1.438
r_mcbond_other	1.435
r_angle_refined_deg	1.425
r_symmetry_nbd_refined	0.278
r_nbd_other	0.248
r_nbd_refined	0.201
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.129
r_symmetry_xyhbond_nbd_refined	0.093
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.076
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5972
Nucleic Acid Atoms
Solvent Atoms	273
Heterogen Atoms	100

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing