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Crystal structure of Human Dihydroorotate Dehydrogenase (DHODH) with 7GF
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 C11DAO, 20.8mM N,N-dimethyldecylamine-N-oxide (DDAO), 2mM DHO, 1.6-1.8 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.44 64.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.875 α = 90 b = 90.875 β = 90 c = 123.17 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 BL19U1 0.987 SSRF BL19U1
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 1.58 41.09 99.86 4 16.3 76164
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 1.58 1.78 99.4 0.997
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 1.58 36.4 76161 4024 99.88 0.17113 0.17036 0.1817 0.18567 0.1915 RANDOM 25.213
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 35.419 r_dihedral_angle_4_deg 17.978 r_dihedral_angle_3_deg 13.001 r_long_range_B_refined 6.924 r_long_range_B_other 6.923 r_scangle_other 6.258 r_dihedral_angle_1_deg 6.082 r_scbond_it 4.343 r_scbond_other 4.343 r_mcangle_other 3.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.419 r_dihedral_angle_4_deg 17.978 r_dihedral_angle_3_deg 13.001 r_long_range_B_refined 6.924 r_long_range_B_other 6.923 r_scangle_other 6.258 r_dihedral_angle_1_deg 6.082 r_scbond_it 4.343 r_scbond_other 4.343 r_mcangle_other 3.143 r_mcangle_it 3.141 r_angle_refined_deg 2.857 r_mcbond_it 2.476 r_mcbond_other 2.322 r_angle_other_deg 1.112 r_chiral_restr 0.168 r_bond_refined_d 0.031 r_gen_planes_refined 0.016 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 2780 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement CrysalisPro data processing HKL-3000 data scaling PHENIX data collection