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Thr110Ala 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 2.36 47.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.493 α = 90 b = 78.885 β = 90 c = 180.091 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 CCD MARMOSAIC 300 mm CCD 2006-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.9793 APS 23-ID-B
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 1.29 32 91.1 0.071 20.5 6.8 166743 166743 16.1
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) 1.29 1.32 49.8 0.363 3 3.1 6718
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 1.29 32 166743 166743 8407 91.1 0.131 0.129 0.1286 0.154 0.154 RANDOM 17.902
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] -0.17 0.15 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.197 r_dihedral_angle_4_deg 14.488 r_sphericity_free 12.383 r_dihedral_angle_3_deg 10.455 r_sphericity_bonded 6.448 r_dihedral_angle_1_deg 6.198 r_scangle_it 5.347 r_scbond_it 4.168 r_mcangle_it 4.087 r_mcbond_it 3.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.197 r_dihedral_angle_4_deg 14.488 r_sphericity_free 12.383 r_dihedral_angle_3_deg 10.455 r_sphericity_bonded 6.448 r_dihedral_angle_1_deg 6.198 r_scangle_it 5.347 r_scbond_it 4.168 r_mcangle_it 4.087 r_mcbond_it 3.59 r_mcbond_other 3.49 r_rigid_bond_restr 2.44 r_angle_refined_deg 1.354 r_angle_other_deg 0.831 r_symmetry_vdw_other 0.243 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.207 r_symmetry_hbond_refined 0.188 r_nbd_other 0.178 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.11 r_chiral_restr 0.083 r_nbtor_other 0.082 r_metal_ion_refined 0.059 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5464 Nucleic Acid Atoms Solvent Atoms 782 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling