☰ Navigation Tabs
Structure of D-3-Hydroxybutyrate Dehydrogenase from Pseudomonas putida
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WMB PDB ENTRY 1WMB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.1 295 17-20 % PEG 1500, 0.2mM calcium chloride, 10mM acetoacetate, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.97 37.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 261.457 α = 90 b = 59.913 β = 113.7 c = 116.523 γ = 90
Symmetry Space Group C 1 2 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 IMAGE PLATE MAR scanner 345 mm plate 2006-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5419
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.02 30 96.7 105219
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 2.02 2.09 74.4 0.593
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 1WMB 2.02 30 104909 5241 96.4 0.202 0.199 0.2539 0.274 0.3125 42.86
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] -2.49 -1.37 3.16 -1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.39 r_dihedral_angle_3_deg 17.869 r_dihedral_angle_4_deg 17.099 r_dihedral_angle_1_deg 7.684 r_scangle_it 4.186 r_scbond_it 3.041 r_angle_refined_deg 2.281 r_mcangle_it 1.683 r_mcbond_it 1.16 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.39 r_dihedral_angle_3_deg 17.869 r_dihedral_angle_4_deg 17.099 r_dihedral_angle_1_deg 7.684 r_scangle_it 4.186 r_scbond_it 3.041 r_angle_refined_deg 2.281 r_mcangle_it 1.683 r_mcbond_it 1.16 r_nbtor_refined 0.31 r_symmetry_hbond_refined 0.264 r_nbd_refined 0.228 r_symmetry_vdw_refined 0.205 r_xyhbond_nbd_refined 0.191 r_chiral_restr 0.168 r_bond_refined_d 0.028 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14526 Nucleic Acid Atoms Solvent Atoms 471 Heterogen Atoms 264
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction