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Structure of D-3-Hydroxybutyrate Dehydrogenase from Pseudomonas putida
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q2Q PDB ENTRY 2Q2Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 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 1.89 34.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.328 α = 90 b = 58.176 β = 92.3 c = 119.382 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) 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 1.9 30 99.5 0.048 20.5 11.3 62236
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 1.9 1.97 98.3 0.154 11 6088
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 (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 2Q2Q 1.9 30 1443 62171 3157 99.33 0.171 0.169 0.1689 0.219 0.2177 RANDOM 18.784
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] -0.1 -0.45 0.68 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.307 r_dihedral_angle_4_deg 16.596 r_dihedral_angle_3_deg 15.638 r_dihedral_angle_1_deg 6.755 r_scangle_it 3.28 r_scbond_it 2.228 r_angle_refined_deg 1.662 r_mcangle_it 1.207 r_mcbond_it 0.765 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.307 r_dihedral_angle_4_deg 16.596 r_dihedral_angle_3_deg 15.638 r_dihedral_angle_1_deg 6.755 r_scangle_it 3.28 r_scbond_it 2.228 r_angle_refined_deg 1.662 r_mcangle_it 1.207 r_mcbond_it 0.765 r_nbtor_refined 0.306 r_nbd_refined 0.212 r_symmetry_hbond_refined 0.195 r_symmetry_vdw_refined 0.192 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.136 r_bond_refined_d 0.016 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7374 Nucleic Acid Atoms Solvent Atoms 447 Heterogen Atoms 132
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection