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Crystal structure of human dihydroorotate dehydrogenase (DHODH) with 18X at 1.86 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JTU
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, 1mM inhibitor
Crystal Properties Matthews coefficient Solvent content 3.47 64.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.319 α = 90 b = 91.319 β = 90 c = 122.824 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 RAYONIX MX-225 2015-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97852 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 1.86 29.04 99.86 1.3 10.7 47711
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.86 1.908 98.99
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 4JTU 1.86 29.04 47711 2553 99.86 0.1609 0.15993 0.1723 0.17893 0.1909 RANDOM 23.267
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 35.536 r_dihedral_angle_4_deg 18.257 r_dihedral_angle_3_deg 13.607 r_long_range_B_refined 7.34 r_long_range_B_other 7.339 r_dihedral_angle_1_deg 6.198 r_scangle_other 5.873 r_scbond_it 4.172 r_scbond_other 4.016 r_mcangle_it 3.434
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.536 r_dihedral_angle_4_deg 18.257 r_dihedral_angle_3_deg 13.607 r_long_range_B_refined 7.34 r_long_range_B_other 7.339 r_dihedral_angle_1_deg 6.198 r_scangle_other 5.873 r_scbond_it 4.172 r_scbond_other 4.016 r_mcangle_it 3.434 r_mcangle_other 3.434 r_mcbond_it 2.535 r_mcbond_other 2.529 r_angle_refined_deg 2.264 r_angle_other_deg 0.978 r_chiral_restr 0.141 r_bond_refined_d 0.026 r_gen_planes_refined 0.013 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 2792 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data scaling Coot model building