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The crystal structure of the ligand-free dihydroorotase from E. coli
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 7 277 20-25% PEG 3350, 0.1M Na HEPES, 0.2M NaF, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.39 48.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.426 α = 90 b = 79.674 β = 90 c = 180.987 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 2004-08-06 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 1.7 17 96.1 0.033 28.7 3.5 82624 79401 2 29.8
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 1.7 1.744 87.5 0.327 2.4 4934
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 (All) 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 1.7 17 82624 79401 3990 96.1 0.176 0.176 0.174 0.1824 0.214 0.2242 RANDOM 34.5
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] 1.33 1.19 -2.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.669 r_dihedral_angle_4_deg 16.189 r_dihedral_angle_3_deg 11.903 r_scangle_it 6.978 r_dihedral_angle_1_deg 6.124 r_scbond_it 5.463 r_mcangle_it 4.047 r_mcbond_it 3.573 r_angle_refined_deg 1.417 r_mcbond_other 1.184
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.669 r_dihedral_angle_4_deg 16.189 r_dihedral_angle_3_deg 11.903 r_scangle_it 6.978 r_dihedral_angle_1_deg 6.124 r_scbond_it 5.463 r_mcangle_it 4.047 r_mcbond_it 3.573 r_angle_refined_deg 1.417 r_mcbond_other 1.184 r_angle_other_deg 0.848 r_symmetry_vdw_other 0.221 r_nbd_refined 0.212 r_symmetry_hbond_refined 0.198 r_nbd_other 0.18 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.145 r_symmetry_vdw_refined 0.103 r_chiral_restr 0.091 r_nbtor_other 0.083 r_metal_ion_refined 0.057 r_bond_refined_d 0.013 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 5345 Nucleic Acid Atoms Solvent Atoms 597 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling