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Dimeric Dihydrodiol Dehydrogenase complexed with inhibitor, Isoascorbic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O4U PDB entry 2O4U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 295 2M ammonium sulphate, 0.1 sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.62 66.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.832 α = 90 b = 122.832 β = 90 c = 121.293 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 IMAGE PLATE MAR scanner 345 mm plate mirrors 2003-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54178
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 2.59 20 99.26 16.5 17256 17128 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) 2.59 2.68 98 3.6284
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2O4U 2.59 20 4 17128 16264 864 98.83 0.2024 0.17035 0.16699 0.1663 0.2341 0.2267 RANDOM 27.089
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] 0.42 0.21 0.42 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.885 r_dihedral_angle_4_deg 19.506 r_dihedral_angle_3_deg 18.7 r_dihedral_angle_1_deg 6.509 r_scangle_it 4.843 r_scbond_it 3.065 r_angle_refined_deg 2.105 r_mcangle_it 1.783 r_mcbond_it 1.062 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.885 r_dihedral_angle_4_deg 19.506 r_dihedral_angle_3_deg 18.7 r_dihedral_angle_1_deg 6.509 r_scangle_it 4.843 r_scbond_it 3.065 r_angle_refined_deg 2.105 r_mcangle_it 1.783 r_mcbond_it 1.062 r_nbtor_refined 0.317 r_nbd_refined 0.233 r_xyhbond_nbd_refined 0.192 r_symmetry_vdw_refined 0.168 r_symmetry_hbond_refined 0.147 r_chiral_restr 0.127 r_bond_refined_d 0.022 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2529 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing