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The crystal structure of Bacillus cereus 3-hydroxyisobutyrate dehydrogenase in complex with NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CKY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 291 22% PEG 6000, 0.1 M HEPES
Crystal Properties Matthews coefficient Solvent content 2.29 46.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.444 α = 90 b = 158.576 β = 90 c = 163.138 γ = 90
Symmetry Space Group P 21 21 21
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 270 2013-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 1.00001 PAL/PLS 7A (6B, 6C1)
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 2.1 30 100 0.08 27.6 6.6 72368
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3CKY 2.1 30 67647 3585 99.66 0.19959 0.1973 0.24269 0.2238 RANDOM 35.8
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] 0.84 -0.53 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.631 r_dihedral_angle_4_deg 17.639 r_dihedral_angle_3_deg 16.605 r_dihedral_angle_1_deg 5.936 r_angle_other_deg 4.284 r_scangle_it 3.008 r_scbond_it 1.892 r_angle_refined_deg 1.483 r_mcangle_it 1.012 r_mcbond_it 0.613
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.631 r_dihedral_angle_4_deg 17.639 r_dihedral_angle_3_deg 16.605 r_dihedral_angle_1_deg 5.936 r_angle_other_deg 4.284 r_scangle_it 3.008 r_scbond_it 1.892 r_angle_refined_deg 1.483 r_mcangle_it 1.012 r_mcbond_it 0.613 r_chiral_restr 0.088 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_gen_planes_other 0.006 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8807 Nucleic Acid Atoms Solvent Atoms 561 Heterogen Atoms 203
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing