2I9P

Crystal structure of human hydroxyisobutyrate dehydrogenase complexed with NAD+

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GF2	PDB entry 2GF2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	25% PEG 3350, 0.2 M NaCl, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.627	α = 90
b = 167.319	β = 107.8
c = 71.089	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	ADSC QUANTUM 210		2006-01-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.00000	ALS	8.2.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.55	62.75	95.7	0.075	12.5	3.2	34330	34330			50

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.55	2.69	89.1		0.52	1.9	2.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2GF2	2.55	50	32570	32570	1728	95.51	0.17616	0.17616	0.17376	0.21983	RANDOM	48.461

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]
-2.4		-1.49	4.54		-3.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.421
r_dihedral_angle_4_deg	20.142
r_dihedral_angle_3_deg	16.432
r_scangle_it	7.09
r_dihedral_angle_1_deg	5.662
r_scbond_it	5.314
r_mcangle_it	2.652
r_mcbond_it	1.714
r_angle_refined_deg	1.352
r_angle_other_deg	0.914
r_mcbond_other	0.498
r_symmetry_hbond_refined	0.391
r_nbd_refined	0.224
r_nbtor_refined	0.184
r_nbd_other	0.181
r_symmetry_vdw_other	0.144
r_xyhbond_nbd_refined	0.12
r_symmetry_vdw_refined	0.106
r_nbtor_other	0.089
r_chiral_restr	0.068
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8375
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	176

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing