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Crystal structure of human dihydroorotate dehydrogenase in complex with lapachol
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 3.63 66.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.46 α = 90 b = 90.46 β = 90 c = 122.66 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 S 2M 2024-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.918400 BESSY 14.2
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 1.31 48.34 100 1 18.45 19.96 139283 22.57
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 1.31 1.39 100 0.412 0.98
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 1.31 48.34 132428 6855 99.94 0.17427 0.17398 0.1835 0.17997 0.1899 RANDOM 20.329
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] 0.28 0.14 0.28 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.976 r_dihedral_angle_4_deg 18.204 r_dihedral_angle_3_deg 11.876 r_dihedral_angle_1_deg 6.123 r_long_range_B_refined 4.727 r_long_range_B_other 4.497 r_scangle_other 2.784 r_mcangle_it 1.89 r_mcangle_other 1.89 r_scbond_it 1.842
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.976 r_dihedral_angle_4_deg 18.204 r_dihedral_angle_3_deg 11.876 r_dihedral_angle_1_deg 6.123 r_long_range_B_refined 4.727 r_long_range_B_other 4.497 r_scangle_other 2.784 r_mcangle_it 1.89 r_mcangle_other 1.89 r_scbond_it 1.842 r_scbond_other 1.841 r_angle_refined_deg 1.456 r_angle_other_deg 1.426 r_mcbond_it 1.184 r_mcbond_other 1.183 r_chiral_restr 0.071 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2727 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement pointless data scaling XDS data reduction PHASER phasing