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The Crystal Structure of the T109S mutant of E. coli Dihydroorotase complexed with an inhibitor 5-fluoroorotate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XGE PDB ENTRY 1XGE chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.25 277 14% 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 2.99 58.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.61 α = 90 b = 72.61 β = 90 c = 176.12 γ = 90
Symmetry Space Group P 41 21 2
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 2.2 30 60.9 0.043 19 6.1 16140 2 73.8
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 2.2 2.24 38.2 0.203 2.1 3.4 462
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 PDB ENTRY 1XGE chain A 2.7 30 13623 10367 490 75.8 0.22023 0.21838 0.2288 0.25677 0.2755 RANDOM 63
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] -0.29 -0.29 0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.841 r_dihedral_angle_4_deg 16.401 r_dihedral_angle_3_deg 12.952 r_dihedral_angle_1_deg 5.346 r_mcangle_it 3.055 r_scangle_it 2.919 r_mcbond_it 2.307 r_scbond_it 1.887 r_angle_refined_deg 0.932 r_angle_other_deg 0.695
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.841 r_dihedral_angle_4_deg 16.401 r_dihedral_angle_3_deg 12.952 r_dihedral_angle_1_deg 5.346 r_mcangle_it 3.055 r_scangle_it 2.919 r_mcbond_it 2.307 r_scbond_it 1.887 r_angle_refined_deg 0.932 r_angle_other_deg 0.695 r_mcbond_other 0.434 r_nbd_refined 0.194 r_symmetry_vdw_other 0.184 r_nbtor_refined 0.166 r_nbd_other 0.156 r_xyhbond_nbd_refined 0.133 r_symmetry_hbond_refined 0.131 r_nbtor_other 0.077 r_metal_ion_refined 0.072 r_symmetry_vdw_refined 0.057 r_chiral_restr 0.052 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2693 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing