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Dihydroorotase from M. jannaschii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MPG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 35% PEG400, 0.1 M Na Hepes pH 7.5, 0.1 M Zn acetate.
Crystal Properties Matthews coefficient Solvent content 3.8 67.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.267 α = 90 b = 111.267 β = 90 c = 101.233 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 2018-12-18 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) 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 1.9 48.18 100 0.239 0.997 9.7 10.9 57394
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 100 3.188 0.31 10
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3MPG 1.9 48.18 1.34 57234 2703 99.77 0.1799 0.1783 0.1779 0.2146 0.2142 Random selection 33.09
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 7.139 f_angle_d 0.9355 f_chiral_restr 0.0595 f_bond_d 0.0077 f_plane_restr 0.0063
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3389 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms 11
Software Software Software Name Purpose PHENIX refinement PHASER phasing XDS data reduction Aimless data scaling Coot model building