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Thr110Val 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 2.36 47.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.447 α = 90 b = 78.968 β = 90 c = 180.534 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 98.4 0.048 24.3 3.6 60822 60822 24.2
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 96.2 0.219 4.2 2.3 4334
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 60822 60822 3091 98.43 0.14914 0.14726 0.1583 0.18482 0.1869 RANDOM 25.814
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] -0.83 0.74 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.208 r_dihedral_angle_4_deg 16.562 r_dihedral_angle_3_deg 11.674 r_scangle_it 7.122 r_dihedral_angle_1_deg 6.164 r_scbond_it 5.399 r_mcangle_it 3.709 r_mcbond_it 3.227 r_angle_refined_deg 1.269 r_mcbond_other 1.056
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.208 r_dihedral_angle_4_deg 16.562 r_dihedral_angle_3_deg 11.674 r_scangle_it 7.122 r_dihedral_angle_1_deg 6.164 r_scbond_it 5.399 r_mcangle_it 3.709 r_mcbond_it 3.227 r_angle_refined_deg 1.269 r_mcbond_other 1.056 r_angle_other_deg 0.815 r_symmetry_vdw_other 0.212 r_nbd_refined 0.208 r_nbd_other 0.178 r_nbtor_refined 0.173 r_symmetry_hbond_refined 0.168 r_xyhbond_nbd_refined 0.135 r_symmetry_vdw_refined 0.099 r_nbtor_other 0.081 r_chiral_restr 0.074 r_metal_ion_refined 0.024 r_bond_refined_d 0.01 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 5384 Nucleic Acid Atoms Solvent Atoms 668 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling