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Thr109Ser dihydroorotase from E. coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XGE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.25 277 17% PEG3350, 0.1M MES, 75mM MgCl2, 0.15M KCl, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.34 47.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.378 α = 90 b = 78.521 β = 90 c = 180.221 γ = 90
Symmetry Space Group P 21 21 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 IMAGE PLATE MAR scanner 345 mm plate mirrors 2005-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.87 40 96.5 0.041 30.4 4.5 59086 59086 24.8
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 1.87 1.92 89.1 0.141 8.7 3.5 3970
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 1XGE 1.87 40 59086 59086 2998 96.48 0.14806 0.14597 0.1572 0.18768 0.1918 RANDOM 26.797
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] -1.23 1.08 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.136 r_dihedral_angle_4_deg 14.704 r_dihedral_angle_3_deg 11.627 r_scangle_it 7.478 r_dihedral_angle_1_deg 6.263 r_scbond_it 5.716 r_mcangle_it 3.902 r_mcbond_it 3.521 r_angle_refined_deg 1.37 r_mcbond_other 1.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.136 r_dihedral_angle_4_deg 14.704 r_dihedral_angle_3_deg 11.627 r_scangle_it 7.478 r_dihedral_angle_1_deg 6.263 r_scbond_it 5.716 r_mcangle_it 3.902 r_mcbond_it 3.521 r_angle_refined_deg 1.37 r_mcbond_other 1.085 r_angle_other_deg 0.825 r_symmetry_vdw_other 0.225 r_nbd_refined 0.214 r_nbd_other 0.181 r_nbtor_refined 0.175 r_symmetry_hbond_refined 0.152 r_xyhbond_nbd_refined 0.123 r_symmetry_vdw_refined 0.105 r_nbtor_other 0.082 r_chiral_restr 0.079 r_metal_ion_refined 0.019 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5348 Nucleic Acid Atoms Solvent Atoms 590 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling