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Human DHODH in complex with ligand H3D3181
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D3G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.8 294.15 0.1 M sodium acetate trihydrate, 1.9 M ammonium sulfate, 30% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 3.65 66.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.636 α = 90 b = 90.636 β = 90 c = 123.06 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 PILATUS 2M 2024-12-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS SIRIUS BEAMLINE MANACA 0.97714 LNLS SIRIUS MANACA
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 1.71 48.47 99.9 0.997 10.1 8.63 63921
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 1.71 1.74 99.6 0.999
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 1.71 48.47 60798 3123 99.94 0.16831 0.16699 0.1793 0.19406 0.2036 RANDOM 24.481
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] 0.37 0.18 0.37 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.109 r_dihedral_angle_2_deg 11.199 r_long_range_B_refined 7.816 r_long_range_B_other 7.487 r_dihedral_angle_1_deg 6.234 r_scangle_other 5.66 r_scbond_it 3.986 r_scbond_other 3.814 r_mcangle_other 3.396 r_mcangle_it 3.392
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.109 r_dihedral_angle_2_deg 11.199 r_long_range_B_refined 7.816 r_long_range_B_other 7.487 r_dihedral_angle_1_deg 6.234 r_scangle_other 5.66 r_scbond_it 3.986 r_scbond_other 3.814 r_mcangle_other 3.396 r_mcangle_it 3.392 r_mcbond_it 2.403 r_mcbond_other 2.386 r_angle_refined_deg 1.856 r_angle_other_deg 0.627 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 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 2716 Nucleic Acid Atoms Solvent Atoms 315 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement pointless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction