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Thr109Ala 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 47.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.341 α = 90 b = 78.498 β = 90 c = 180.504 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 2005-11-04 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 97.2 0.051 18 4.7 56793 56793 26.4
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 94.3 0.283 4.5 3.5 3970
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 1.9 40 56793 56793 2879 97.24 0.14928 0.14715 0.1571 0.18848 0.1914 RANDOM 26.767
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 1.25 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.242 r_dihedral_angle_4_deg 15.693 r_dihedral_angle_3_deg 11.759 r_dihedral_angle_1_deg 6.4 r_scangle_it 6.049 r_scbond_it 4.335 r_mcangle_it 4.283 r_mcbond_it 3.951 r_angle_refined_deg 1.389 r_mcbond_other 1.288
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.242 r_dihedral_angle_4_deg 15.693 r_dihedral_angle_3_deg 11.759 r_dihedral_angle_1_deg 6.4 r_scangle_it 6.049 r_scbond_it 4.335 r_mcangle_it 4.283 r_mcbond_it 3.951 r_angle_refined_deg 1.389 r_mcbond_other 1.288 r_angle_other_deg 0.835 r_symmetry_vdw_other 0.251 r_xyhbond_nbd_other 0.216 r_nbd_refined 0.214 r_nbd_other 0.182 r_symmetry_hbond_refined 0.178 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.137 r_symmetry_vdw_refined 0.12 r_chiral_restr 0.083 r_nbtor_other 0.083 r_metal_ion_refined 0.023 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_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 5356 Nucleic Acid Atoms Solvent Atoms 505 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling