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Human DHODH bound to inhibitor IPP/CNRS-A017
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MUT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.8 293 32% PEG 400
0.2M KSCN
0.2M NaBr
0.1M acetate 4.8
Crystal Properties Matthews coefficient Solvent content 3.38 63.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.565 α = 90 b = 90.565 β = 90 c = 122.387 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 EIGER X 16M 2019-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.999987 SLS X06SA
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 1.8 48.293 100 0.999 17.6 9 54364
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 1.8 1.84 0.691
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5MUT 1.8 48.25 54321 2621 99.932 0.183 0.1817 0.1923 0.2026 0.2117 29.245
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] 0.418 0.209 0.418 -1.357
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.604 r_dihedral_angle_4_deg 15.815 r_dihedral_angle_3_deg 13.25 r_dihedral_angle_1_deg 6.464 r_lrange_it 4.991 r_lrange_other 4.908 r_scangle_it 3.441 r_scangle_other 3.44 r_mcangle_it 2.344 r_mcangle_other 2.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.604 r_dihedral_angle_4_deg 15.815 r_dihedral_angle_3_deg 13.25 r_dihedral_angle_1_deg 6.464 r_lrange_it 4.991 r_lrange_other 4.908 r_scangle_it 3.441 r_scangle_other 3.44 r_mcangle_it 2.344 r_mcangle_other 2.338 r_scbond_it 2.147 r_scbond_other 2.146 r_mcbond_it 1.519 r_mcbond_other 1.518 r_angle_refined_deg 1.365 r_angle_other_deg 1.269 r_nbd_other 0.234 r_symmetry_xyhbond_nbd_refined 0.204 r_nbd_refined 0.195 r_symmetry_nbd_other 0.176 r_nbtor_refined 0.152 r_symmetry_nbd_refined 0.131 r_xyhbond_nbd_refined 0.128 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.062 r_gen_planes_refined 0.007 r_bond_refined_d 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2613 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing