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High-Resolution Structure of Human DHODH for Molecular Replacement in Fragment Screening Campaign
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5K9C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.8 293.15 0.1 M sodium acetate trihydrate pH 4.8, 1.8 M ammonium sulfate and 30% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 3.87 68.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.597 α = 90 b = 90.597 β = 90 c = 123.232 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 PILATUS3 6M 2023-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 1.6 48.46 99.9 0.971 11.3 9.8 77597 1
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 1.6 1.63 100 0.595 1.3 9.9
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 NONE 1.6 48.46 77550 3937 99.915 0.181 0.1802 0.1802 0.1968 0.1968 23.286
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] 0.006 0.003 0.006 -0.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.656 r_dihedral_angle_3_deg 12.253 r_dihedral_angle_2_deg 9.306 r_dihedral_angle_1_deg 5.811 r_lrange_it 5.687 r_scangle_it 2.715 r_mcangle_it 1.737 r_scbond_it 1.662 r_mcbond_it 1.07 r_angle_refined_deg 1.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.656 r_dihedral_angle_3_deg 12.253 r_dihedral_angle_2_deg 9.306 r_dihedral_angle_1_deg 5.811 r_lrange_it 5.687 r_scangle_it 2.715 r_mcangle_it 1.737 r_scbond_it 1.662 r_mcbond_it 1.07 r_angle_refined_deg 1.067 r_nbtor_refined 0.304 r_nbd_refined 0.207 r_symmetry_nbd_refined 0.185 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.077 r_symmetry_xyhbond_nbd_refined 0.075 r_gen_planes_refined 0.005 r_bond_refined_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2602 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement PHASER phasing XDS data reduction