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Crystal structure of human dihydroorotate dehydrogenase (DHODH) with DH03A347
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JS3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 293 0.1M acetate pH 4.8, 40 mM UDAO, 20.8 mM N,N-dimethyldecylamine-N-oxide (DDAO), 2mM DHO, 1.6-1.8M ammonium sulfate, 1 mM inhibitor, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.41 63.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.65 α = 90 b = 90.65 β = 90 c = 122.45 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 315r 2014-06-29 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 2.71 66.09 94.7 16278 15409 2 2
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 2.71 2.86
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 4JS3 2.71 66.09 16278 15409 857 99.69 0.16662 0.16325 0.174 0.2278 0.2284 RANDOM 17.782
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] 0.04 0.02 0.04 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.403 r_dihedral_angle_4_deg 18.21 r_dihedral_angle_3_deg 16.077 r_dihedral_angle_1_deg 6.433 r_mcangle_other 2.621 r_mcangle_it 2.62 r_scbond_it 2.438 r_angle_refined_deg 2.005 r_mcbond_it 1.555 r_mcbond_other 1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.403 r_dihedral_angle_4_deg 18.21 r_dihedral_angle_3_deg 16.077 r_dihedral_angle_1_deg 6.433 r_mcangle_other 2.621 r_mcangle_it 2.62 r_scbond_it 2.438 r_angle_refined_deg 2.005 r_mcbond_it 1.555 r_mcbond_other 1.55 r_angle_other_deg 0.876 r_chiral_restr 0.086 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2792 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 99
Software Software Software Name Purpose HKL-2000 data collection auto model building REFMAC refinement HKL-2000 data reduction iMOSFLM data reduction auto phasing