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Human DHODH in complex with ligand H3D2856
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PRM
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 3.63 66.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.938 α = 90 b = 90.938 β = 90 c = 123.703 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 9M 2023-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980112 SOLEIL PROXIMA 2
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 2.3 48.64 100 0.994 7.7 20.3 26893
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 2.3 2.38 100 0.375 1.2 20.7
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 2.3 48.6 25469 1388 99.99 0.16934 0.16715 0.1674 0.21148 0.2112 RANDOM 37.768
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] 0.26 0.13 0.26 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.72 r_dihedral_angle_2_deg 12.369 r_long_range_B_refined 11.621 r_scbond_it 7.228 r_dihedral_angle_1_deg 6.65 r_mcangle_it 5.734 r_mcbond_it 4.102 r_angle_refined_deg 2.086 r_chiral_restr 0.13 r_bond_refined_d 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.72 r_dihedral_angle_2_deg 12.369 r_long_range_B_refined 11.621 r_scbond_it 7.228 r_dihedral_angle_1_deg 6.65 r_mcangle_it 5.734 r_mcbond_it 4.102 r_angle_refined_deg 2.086 r_chiral_restr 0.13 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2540 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 103
Software Software Software Name Purpose REFMAC refinement pointless data scaling XDS data reduction PHASER phasing