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Human DHODH in Complex with QC6352
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SYP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 34% PEG 400
0.2 M KSCN
0.2 M NaBr
0.1M acetate pH 4.8
Crystal Properties Matthews coefficient Solvent content 3.62 66.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.384 α = 90 b = 90.384 β = 90 c = 122.511 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 EIGER2 X 16M 2025-01-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97628 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.95 66.05 100 0.99 13.1 20.4 42816
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 0.716 1.8 21.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.95 66.05 40632 2111 99.92 0.17867 0.1776 0.1917 0.19805 0.2129 RANDOM 34.668
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] 0.25 0.12 0.25 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.131 r_dihedral_angle_2_deg 9.946 r_dihedral_angle_1_deg 6.396 r_long_range_B_refined 6.011 r_long_range_B_other 5.979 r_scangle_other 4.138 r_mcangle_other 2.806 r_mcangle_it 2.801 r_scbond_it 2.775 r_scbond_other 2.668
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.131 r_dihedral_angle_2_deg 9.946 r_dihedral_angle_1_deg 6.396 r_long_range_B_refined 6.011 r_long_range_B_other 5.979 r_scangle_other 4.138 r_mcangle_other 2.806 r_mcangle_it 2.801 r_scbond_it 2.775 r_scbond_other 2.668 r_mcbond_it 1.899 r_mcbond_other 1.893 r_angle_refined_deg 1.32 r_angle_other_deg 0.448 r_chiral_restr 0.065 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2690 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction MOLREP phasing