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Crystal structure of human dihydroorotate dehydrogenase (DHODH) with No.33 compound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JTS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 293 0.1M acetate, 40mM UDAO, 20.8mM N,N-dimethyldecylamine-N-oxide (DDAO), 2mM DHO, 1.6-1.8M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.43 64.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.721 α = 90 b = 90.721 β = 90 c = 123.02 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 293 CCD ADSC QUANTUM 315r 2014-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 1.0 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.79 28.64 99.89 11.7 10.1 53848
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.79 1.82 99.89 0.513 5.7 10.1
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 4JTS 1.79 28.64 53848 1995 99.89 0.15545 0.15461 0.17822 0.1888 RANDOM 22.646
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 35.586 r_dihedral_angle_4_deg 20.642 r_dihedral_angle_3_deg 12.866 r_long_range_B_other 8.646 r_long_range_B_refined 8.644 r_scangle_other 6.786 r_dihedral_angle_1_deg 6.491 r_scbond_it 4.915 r_scbond_other 4.913 r_mcangle_it 3.332
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.586 r_dihedral_angle_4_deg 20.642 r_dihedral_angle_3_deg 12.866 r_long_range_B_other 8.646 r_long_range_B_refined 8.644 r_scangle_other 6.786 r_dihedral_angle_1_deg 6.491 r_scbond_it 4.915 r_scbond_other 4.913 r_mcangle_it 3.332 r_mcangle_other 3.331 r_angle_refined_deg 2.466 r_mcbond_it 2.362 r_mcbond_other 2.36 r_angle_other_deg 0.991 r_chiral_restr 0.141 r_bond_refined_d 0.026 r_gen_planes_refined 0.014 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 2785 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP model building MOLREP phasing