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Crystal structure of human hydroxyisobutyrate dehydrogenase complexed with NAD+
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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) 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 0.1846 0.21983 0.2231 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
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