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Crystal structure of Mammalian Dimeric Dihydrodiol Dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O48
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 295 1.5M ammonium phosphate, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.63 66.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.177 α = 90 b = 123.177 β = 90 c = 121.127 γ = 120
Symmetry Space Group P 61 2 2
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 315 Bent conical Si-mirror (Rh coated) 2001-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 1.00000 APS 14-BM-C
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 19.9 99.7 0.055 17.9 7.2 70365 37154 1 2
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 2.07 99.9 11.77 6990
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2O48 2 19.9 4 37093 35197 1853 99.73 0.1755 0.16306 0.16149 0.19333 0.2236 RANDOM 22.174
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] 0.22 0.11 0.22 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.61 r_dihedral_angle_4_deg 14.704 r_dihedral_angle_3_deg 13.777 r_dihedral_angle_1_deg 5.672 r_scangle_it 3.618 r_scbond_it 2.294 r_angle_refined_deg 1.334 r_mcangle_it 1.294 r_mcbond_it 0.855 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.61 r_dihedral_angle_4_deg 14.704 r_dihedral_angle_3_deg 13.777 r_dihedral_angle_1_deg 5.672 r_scangle_it 3.618 r_scbond_it 2.294 r_angle_refined_deg 1.334 r_mcangle_it 1.294 r_mcbond_it 0.855 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.286 r_symmetry_hbond_refined 0.226 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.196 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2529 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling Coot model building