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dihydroorotate dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JUE PDB accession code 1JUE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 298 0.4 ul protein 14.1 mg/ml
0.4 ul crystallization buffer, 40% PEG 1000, 0.1M Na Citrate, 0.1M KBr, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2 36.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.605 α = 90 b = 162.63 β = 90 c = 163.07 γ = 90
Symmetry Space Group C 2 2 21
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 210 2005-09-05 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 0.9201 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (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 1.95 163 96.2 0.107 0.107 6 4.4 76097
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.06 0.428 0.428 1.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB accession code 1JUE 1.95 50 75972 72158 3814 96 0.1916 0.18894 0.24243 0.187 RANDOM 14.022
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] -0.78 1.08 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.521 r_dihedral_angle_4_deg 15.886 r_dihedral_angle_3_deg 13.928 r_dihedral_angle_1_deg 6.255 r_scangle_it 2.256 r_scbond_it 1.495 r_angle_refined_deg 1.326 r_angle_other_deg 0.837 r_mcangle_it 0.821 r_mcbond_it 0.714
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.521 r_dihedral_angle_4_deg 15.886 r_dihedral_angle_3_deg 13.928 r_dihedral_angle_1_deg 6.255 r_scangle_it 2.256 r_scbond_it 1.495 r_angle_refined_deg 1.326 r_angle_other_deg 0.837 r_mcangle_it 0.821 r_mcbond_it 0.714 r_symmetry_vdw_refined 0.323 r_symmetry_hbond_refined 0.294 r_symmetry_vdw_other 0.259 r_nbd_refined 0.196 r_nbd_other 0.178 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.168 r_mcbond_other 0.127 r_nbtor_other 0.083 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9572 Nucleic Acid Atoms Solvent Atoms 638 Heterogen Atoms 203
Software Software Software Name Purpose SCALA data scaling PDB_EXTRACT data extraction REFMAC refinement CCP4 data scaling MOLREP phasing