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Crystal structure of human DHODH with TAK-632
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OQV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.2 293 Sodium Phosphate
Crystal Properties Matthews coefficient Solvent content 3.05 59.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.668 α = 90 b = 113.668 β = 90 c = 113.668 γ = 90
Symmetry Space Group P 21 3
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 MARMOSAIC 300 mm CCD 2019-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.978720 APS 21-ID-G
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 2.7 50 99.9 0.999 21.58 20 13751
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 2.7 2.85 99.8 0.711 2.05 15
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 4OQV 2.7 46.45 12947 743 99.43 0.23328 0.22985 0.2342 0.29394 0.2912 RANDOM 67.459
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.1 r_dihedral_angle_3_deg 18.771 r_dihedral_angle_4_deg 14.578 r_long_range_B_other 9.25 r_long_range_B_refined 9.249 r_dihedral_angle_1_deg 6.517 r_mcangle_it 6.338 r_mcangle_other 6.275 r_scangle_other 5.889 r_mcbond_it 3.992
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.1 r_dihedral_angle_3_deg 18.771 r_dihedral_angle_4_deg 14.578 r_long_range_B_other 9.25 r_long_range_B_refined 9.249 r_dihedral_angle_1_deg 6.517 r_mcangle_it 6.338 r_mcangle_other 6.275 r_scangle_other 5.889 r_mcbond_it 3.992 r_mcbond_other 3.991 r_scbond_it 3.724 r_scbond_other 3.683 r_angle_refined_deg 1.264 r_angle_other_deg 1.115 r_chiral_restr 0.032 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_gen_planes_other 0.001 r_bond_other_d 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 2769 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement MOLREP phasing XDS data reduction Coot model building XDS data scaling