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Thr110Ser 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% PEG 3350, 0.1M MES, 75mM MgCl2, 0.15M KCl, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.35 47.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.447 α = 90 b = 78.79 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 2005-06-08 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 1.9 40 96.6 0.077 18.1 3.5 56580 56580 25.5
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 1.9 1.95 95.7 0.311 3.1 2.3 4062
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 Refinement THROUGHOUT 1XGE 1.9 40 56580 56580 2866 96.56 0.15171 0.14928 0.1598 0.19805 0.203 RANDOM 28.209
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] -0.48 0.24 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.269 r_dihedral_angle_4_deg 15.73 r_dihedral_angle_3_deg 12.322 r_scangle_it 8.439 r_scbond_it 6.471 r_dihedral_angle_1_deg 6.449 r_mcangle_it 4.569 r_mcbond_it 4.18 r_angle_refined_deg 1.466 r_mcbond_other 1.327
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.269 r_dihedral_angle_4_deg 15.73 r_dihedral_angle_3_deg 12.322 r_scangle_it 8.439 r_scbond_it 6.471 r_dihedral_angle_1_deg 6.449 r_mcangle_it 4.569 r_mcbond_it 4.18 r_angle_refined_deg 1.466 r_mcbond_other 1.327 r_angle_other_deg 0.861 r_symmetry_vdw_other 0.256 r_nbd_refined 0.213 r_nbd_other 0.184 r_symmetry_hbond_refined 0.18 r_nbtor_refined 0.177 r_symmetry_vdw_refined 0.162 r_xyhbond_nbd_refined 0.153 r_chiral_restr 0.086 r_nbtor_other 0.084 r_metal_ion_refined 0.051 r_bond_refined_d 0.014 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 5338 Nucleic Acid Atoms Solvent Atoms 572 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling