2I9P

Crystal structure of human hydroxyisobutyrate dehydrogenase complexed with NAD+


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GF2PDB entry 2GF2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529325% PEG 3350, 0.2 M NaCl, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0740.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.627α = 90
b = 167.319β = 107.8
c = 71.089γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-01-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.11.00000ALS8.2.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.5562.7595.70.07512.53.2343303433050
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.552.6989.10.521.92.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2GF22.55503257032570172895.510.176160.176160.173760.21983RANDOM48.461
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]
-2.4-1.494.54-3.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.421
r_dihedral_angle_4_deg20.142
r_dihedral_angle_3_deg16.432
r_scangle_it7.09
r_dihedral_angle_1_deg5.662
r_scbond_it5.314
r_mcangle_it2.652
r_mcbond_it1.714
r_angle_refined_deg1.352
r_angle_other_deg0.914
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.421
r_dihedral_angle_4_deg20.142
r_dihedral_angle_3_deg16.432
r_scangle_it7.09
r_dihedral_angle_1_deg5.662
r_scbond_it5.314
r_mcangle_it2.652
r_mcbond_it1.714
r_angle_refined_deg1.352
r_angle_other_deg0.914
r_mcbond_other0.498
r_symmetry_hbond_refined0.391
r_nbd_refined0.224
r_nbtor_refined0.184
r_nbd_other0.181
r_symmetry_vdw_other0.144
r_xyhbond_nbd_refined0.12
r_symmetry_vdw_refined0.106
r_nbtor_other0.089
r_chiral_restr0.068
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms8375
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms176

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
CCP4data scaling
PHASERphasing