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Human DHODH in complex with ligand H3D3186
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, and 30% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 3.65 66.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.544 α = 90 b = 90.544 β = 90 c = 123.365 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 2024-06-12 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 1.74 48.48 99.8 0.996 9.3 18.927 59921
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 1.74 1.78 96.7 0.451 0.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.745 48.48 59921 2858 99.815 0.168 0.167 0.1674 0.1856 0.1859 25.782
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] 0.358 0.179 0.358 -1.162
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.138 r_dihedral_angle_3_deg 12.699 r_dihedral_angle_2_deg 12.07 r_lrange_it 7.552 r_lrange_other 7.222 r_dihedral_angle_1_deg 6.121 r_scangle_it 5.237 r_scangle_other 4.991 r_scbond_it 3.364 r_scbond_other 3.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.138 r_dihedral_angle_3_deg 12.699 r_dihedral_angle_2_deg 12.07 r_lrange_it 7.552 r_lrange_other 7.222 r_dihedral_angle_1_deg 6.121 r_scangle_it 5.237 r_scangle_other 4.991 r_scbond_it 3.364 r_scbond_other 3.11 r_mcangle_other 3.013 r_mcangle_it 3.012 r_mcbond_it 1.993 r_mcbond_other 1.969 r_angle_refined_deg 1.573 r_angle_other_deg 0.549 r_symmetry_nbd_refined 0.304 r_nbd_refined 0.227 r_symmetry_xyhbond_nbd_refined 0.218 r_nbd_other 0.204 r_xyhbond_nbd_refined 0.195 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.178 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.075 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2707 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms 127
Software Software Software Name Purpose REFMAC refinement XDS data reduction pointless data scaling PHASER phasing