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Complex of Dihydroorotase from M. jannaschii with Carbamoyl Aspartate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7UOF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 Reservoirs: 35% PEG400, 0.1 M Zn acetate and 0.1 M Na Mes pH 6.5. Drops: 2 ul protein 6.7 mg/ml, 1 ul reservoir, 0.5 ul dihydroorotate stock of 65 mM
Crystal Properties Matthews coefficient Solvent content 3.81 67.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.38 α = 90 b = 111.38 β = 90 c = 101.22 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 CMOS RDI CMOS_8M 2019-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.0 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 48.23 99.3 0.119 0.129 0.048 0.998 12.1 6.9 59804 25.79
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 1.91 93.7 1.635 1.812 0.764 0.371 0.9 5.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.87 48.23 1.34 59680 2964 99.05 0.1694 0.1685 0.1863 0.1693 30.85
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.3022 f_angle_d 0.9555 f_chiral_restr 0.0607 f_bond_d 0.0075 f_plane_restr 0.0067
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3389 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 23
Software Software Software Name Purpose PHASER phasing PHENIX refinement XDS data reduction Aimless data scaling Coot model building