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Structure of Human Dihydroorotate Dehydrogenase with a Bound Inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D3G PDB ENTRY 1D3G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1 M SODIUM ACETATE (PH 4.8), 2.4-2.6 M AMMONIUM SULPHATE, 40 MM C11DAO, 20 MM DDAO.
Crystal Properties Matthews coefficient Solvent content 3.69 66.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.79 α = 90 b = 90.79 β = 90 c = 123.491 γ = 120
Symmetry Space Group P 32 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 CCD ADSC CCD 2009-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 1.55 30.87 99.8 0.08 14 5.3 85643 13.658
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 1.55 1.63 100 0.44 3.7 5.4
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 1D3G 1.55 78.63 81242 4279 99.69 0.16029 0.15939 0.1682 0.17744 0.1832 RANDOM 13.179
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] 0.3 0.15 0.3 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.14 r_dihedral_angle_4_deg 17.269 r_dihedral_angle_3_deg 12.046 r_dihedral_angle_1_deg 5.571 r_scangle_it 4.799 r_scbond_it 2.84 r_mcangle_it 1.887 r_angle_refined_deg 1.567 r_mcbond_it 1.022 r_angle_other_deg 0.941
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.14 r_dihedral_angle_4_deg 17.269 r_dihedral_angle_3_deg 12.046 r_dihedral_angle_1_deg 5.571 r_scangle_it 4.799 r_scbond_it 2.84 r_mcangle_it 1.887 r_angle_refined_deg 1.567 r_mcbond_it 1.022 r_angle_other_deg 0.941 r_mcbond_other 0.276 r_chiral_restr 0.1 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2693 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing