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Crystal structure of human DHODH in complex with Lapachol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZF4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.9 293 100 mM SODIUM ACETATE, 1.8-1.9 M, AMMONIUM SULPHATE, 40 mM C11DAO,
20.8 mM DDAO, 2 mM DIHYDROOROTATE, PH 4.9
Crystal Properties Matthews coefficient Solvent content 3.65 66.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.364 α = 90 b = 90.364 β = 90 c = 123.002 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 CCD ADSC QUANTUM 315 2011-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98000 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.75 50 100 0.063 0.929 12 9.7 59153
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 100 0.574 0.76 4.4 9.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5ZF4 1.75 19.89 55945 2978 99.69 0.1566 0.15581 0.1686 0.17077 0.1822 RANDOM 24.057
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.985 r_dihedral_angle_4_deg 19.695 r_dihedral_angle_3_deg 12.779 r_dihedral_angle_1_deg 6.689 r_long_range_B_refined 5.877 r_long_range_B_other 5.737 r_scangle_other 3.798 r_mcangle_it 2.364 r_mcangle_other 2.364 r_scbond_it 2.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.985 r_dihedral_angle_4_deg 19.695 r_dihedral_angle_3_deg 12.779 r_dihedral_angle_1_deg 6.689 r_long_range_B_refined 5.877 r_long_range_B_other 5.737 r_scangle_other 3.798 r_mcangle_it 2.364 r_mcangle_other 2.364 r_scbond_it 2.319 r_scbond_other 2.318 r_mcbond_it 1.487 r_angle_refined_deg 1.478 r_mcbond_other 1.468 r_angle_other_deg 0.978 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2797 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing