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Structure of DHODH in Complex with Ligand 17
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8DHG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.8 293 0.10 M NaAcetat_pH4,8 2.30 M (NH4)2SO4 30 % Glycerol, 18% (w/v) PEG 4000, 0,1M Na3Citrate pH=5.75
Crystal Properties Matthews coefficient Solvent content 3.55 65.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.744 α = 90 b = 90.744 β = 90 c = 122.713 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 6M 2019-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.93 78.59 95.6 0.065 0.084 0.997 11.1 2.2 42552
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 2.18 0.501 0.657 0.729 2.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 8DHG 1.93 78.59 40510 2042 95.61 0.16915 0.16764 0.19903 0.2078 RANDOM 22.087
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] -0.11 -0.05 -0.11 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.895 r_dihedral_angle_4_deg 18.439 r_dihedral_angle_3_deg 13.06 r_long_range_B_refined 8.431 r_long_range_B_other 8.347 r_scangle_other 7.196 r_scbond_it 7.019 r_scbond_other 7.008 r_dihedral_angle_1_deg 6.151 r_mcangle_it 3.975
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.895 r_dihedral_angle_4_deg 18.439 r_dihedral_angle_3_deg 13.06 r_long_range_B_refined 8.431 r_long_range_B_other 8.347 r_scangle_other 7.196 r_scbond_it 7.019 r_scbond_other 7.008 r_dihedral_angle_1_deg 6.151 r_mcangle_it 3.975 r_mcangle_other 3.974 r_mcbond_it 3.176 r_mcbond_other 3.134 r_angle_refined_deg 1.99 r_angle_other_deg 1.437 r_chiral_restr 0.119 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.005 r_gen_planes_other 0.003 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 2712 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 127
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement PHASER phasing