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The crystal structure of E. coli dihydroorotase complexed with HDDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XGE PDB entry 1XGE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 15-20% PEG 3350, 0.1M MES, 75mM MgCl2, 150mM KCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.39 48.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.585 α = 90 b = 79.628 β = 90 c = 180.652 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 ADSC QUANTUM 315 Bending magnet 2006-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9002 APS 14-BM-C
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 30 90.3 0.08 9.9 6.4 51220 46251 2 27.8
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 2.05 91 0.345 2.3 6.3 3201
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 PDB entry 1XGE 2 30 51220 46251 2384 90.3 0.18272 0.17989 0.1892 0.23533 0.2401 RANDOM 36.045
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] 1.89 1.9 -3.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.84 r_dihedral_angle_4_deg 16.113 r_dihedral_angle_3_deg 13.356 r_dihedral_angle_1_deg 6.432 r_scangle_it 2.297 r_scbond_it 1.554 r_angle_refined_deg 1.394 r_mcangle_it 0.869 r_angle_other_deg 0.844 r_mcbond_it 0.742
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.84 r_dihedral_angle_4_deg 16.113 r_dihedral_angle_3_deg 13.356 r_dihedral_angle_1_deg 6.432 r_scangle_it 2.297 r_scbond_it 1.554 r_angle_refined_deg 1.394 r_mcangle_it 0.869 r_angle_other_deg 0.844 r_mcbond_it 0.742 r_symmetry_vdw_other 0.231 r_nbd_refined 0.203 r_symmetry_hbond_refined 0.184 r_nbd_other 0.181 r_nbtor_refined 0.173 r_mcbond_other 0.149 r_xyhbond_nbd_refined 0.138 r_metal_ion_refined 0.104 r_symmetry_vdw_refined 0.085 r_chiral_restr 0.083 r_nbtor_other 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5388 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling