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Thr109Gly 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 2.33 47.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.435 α = 90 b = 78.193 β = 90 c = 179.961 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 2005-04-30 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 1.87 40 91.9 0.048 34.1 4.6 56036 56036 25.2
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 1.87 1.92 91.7 0.152 8.7 3.9 4069
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 1.87 40 56036 56036 2835 91.94 0.15454 0.15236 0.1621 0.19612 0.2004 RANDOM 29.116
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] -1.17 1.93 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.353 r_dihedral_angle_4_deg 16.52 r_dihedral_angle_3_deg 12.722 r_scangle_it 7.609 r_dihedral_angle_1_deg 6.267 r_scbond_it 6.085 r_mcangle_it 4.356 r_mcbond_it 3.744 r_angle_refined_deg 1.443 r_mcbond_other 1.225
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.353 r_dihedral_angle_4_deg 16.52 r_dihedral_angle_3_deg 12.722 r_scangle_it 7.609 r_dihedral_angle_1_deg 6.267 r_scbond_it 6.085 r_mcangle_it 4.356 r_mcbond_it 3.744 r_angle_refined_deg 1.443 r_mcbond_other 1.225 r_angle_other_deg 0.84 r_symmetry_vdw_other 0.228 r_nbd_refined 0.214 r_nbd_other 0.182 r_nbtor_refined 0.178 r_symmetry_vdw_refined 0.166 r_xyhbond_nbd_refined 0.148 r_symmetry_hbond_refined 0.142 r_chiral_restr 0.087 r_nbtor_other 0.084 r_metal_ion_refined 0.024 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5308 Nucleic Acid Atoms Solvent Atoms 583 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling