7D5M | pdb_00007d5m

Crystal structure of inositol dehydrogenase homolog complexed with NAD+ 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	7	293	0.1 M ammonium tartrate dibasic, pH 7.0, 12% (w/v) PEG 3350, 10 mM NAD+

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.25	α = 90
b = 107.997	β = 90
c = 156.759	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	95	CCD	ADSC QUANTUM 210		2011-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	0.9800	Photon Factory	BL-5A

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	1.75	50	99.7	0.041	0.997	33.1	3.6		46835

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	1.75	1.78			0.208	0.95	6	2.7

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	1.75	37.663	46817	2274	99.541	0.18	0.1789	0.19	0.1933	0.2	15.538

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]
1.523			-0.83		-0.692

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.432
r_dihedral_angle_4_deg	17.127
r_dihedral_angle_3_deg	12.502
r_dihedral_angle_1_deg	7.026
r_lrange_it	3.103
r_lrange_other	3.03
r_scangle_it	2.119
r_scangle_other	2.118
r_angle_other_deg	1.383
r_scbond_it	1.366
r_scbond_other	1.366
r_mcangle_it	1.338
r_angle_refined_deg	1.337
r_mcangle_other	1.337
r_mcbond_it	0.82
r_mcbond_other	0.82
r_symmetry_nbd_refined	0.244
r_nbd_other	0.208
r_nbd_refined	0.197
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.161
r_xyhbond_nbd_refined	0.12
r_symmetry_xyhbond_nbd_refined	0.085
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.07
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3027
Nucleic Acid Atoms
Solvent Atoms	273
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing