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HUMAN DIHYDROOROTATE DEHYDROGENASE IN COMPLEX WITH NOVEL INHIBITOR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OQV PDB ENTRY 4OQV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 293 30% glycerol, 100 mM Sodium acetate pH 4.8, 2 M Ammoniumsulphate
Crystal Properties Matthews coefficient Solvent content 3.67 66.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.86 α = 90 b = 90.86 β = 90 c = 122.7 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 PIXEL DECTRIS PILATUS3 6M 2015-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
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 1.7 30 99.1 0.06 23.4 10.7 64865
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 1.7 1.74 86.1 0.46 4.3 7.6
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 4OQV 1.7 30 61296 3227 99.31 0.10697 0.10535 0.1056 0.13809 0.1365 RANDOM 26.525
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] 0.02 0.02 0.02 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.037 r_sphericity_free 32.914 r_sphericity_bonded 18.716 r_dihedral_angle_4_deg 17.797 r_dihedral_angle_3_deg 12.858 r_scangle_other 8.602 r_scbond_it 7.969 r_scbond_other 7.966 r_long_range_B_refined 7.217 r_long_range_B_other 7.216
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.037 r_sphericity_free 32.914 r_sphericity_bonded 18.716 r_dihedral_angle_4_deg 17.797 r_dihedral_angle_3_deg 12.858 r_scangle_other 8.602 r_scbond_it 7.969 r_scbond_other 7.966 r_long_range_B_refined 7.217 r_long_range_B_other 7.216 r_dihedral_angle_1_deg 6.284 r_rigid_bond_restr 6.134 r_mcangle_it 6.086 r_mcangle_other 6.086 r_mcbond_it 5.435 r_mcbond_other 5.397 r_angle_refined_deg 2.284 r_angle_other_deg 1.01 r_chiral_restr 0.136 r_bond_refined_d 0.021 r_gen_planes_refined 0.013 r_gen_planes_other 0.002 r_bond_other_d 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2804 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 131
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement