☰ 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 2Q2Q PDB ENTRY 2Q2Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.1 295 20 % PEG1500, 0.2 mM calcium chloride, 10mM acetoacetate, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.94 36.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.684 α = 90 b = 58.814 β = 93.72 c = 119.462 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 2006-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 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 2.12 30 99.1 0.067 17.2 9.9 1202 46410 34.4
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 2.12 2.2 94.4 0.369 7.6 4368
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2Q2Q 2.12 30 46306 2340 98.95 0.184 0.181 0.18 0.247 0.2448 RANDOM 32.852
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] -0.57 0.47 1.79 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.506 r_dihedral_angle_4_deg 20.192 r_dihedral_angle_3_deg 17.487 r_dihedral_angle_1_deg 7.583 r_scangle_it 4.048 r_scbond_it 2.931 r_angle_refined_deg 2.027 r_mcangle_it 1.587 r_mcbond_it 1.106 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.506 r_dihedral_angle_4_deg 20.192 r_dihedral_angle_3_deg 17.487 r_dihedral_angle_1_deg 7.583 r_scangle_it 4.048 r_scbond_it 2.931 r_angle_refined_deg 2.027 r_mcangle_it 1.587 r_mcbond_it 1.106 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.26 r_nbd_refined 0.216 r_symmetry_hbond_refined 0.192 r_xyhbond_nbd_refined 0.185 r_chiral_restr 0.16 r_bond_refined_d 0.028 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7392 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection