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Rubella virus p150 macro domain (apo)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IQY human protein-proximal ADP-ribosyl-hydrolase MacroD2, chain B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 291 14.4% PEG 6K, 1.26 M LiCl, 0.1 M Bicine pH 9, supplemented with 10% glycerol for prior to freezing
Crystal Properties Matthews coefficient Solvent content 2.71 54.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.682 α = 90 b = 87.569 β = 90 c = 135.507 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 XE 16M Focussing mirrors 2020-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.72 64.1 91.3 0.112 0.052 0.997 9.9 5.3 23298 21.66
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.723 1.949 53.5 1.03 0.514 0.613 1.6 4.6
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-Work (DCC) R-Free (Depositor) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.72 43 1.33 23294 1183 50.62 0.1883 0.1862 0.1832 0.2283 32.94
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 5.7651 f_angle_d 0.8181 f_chiral_restr 0.0461 f_plane_restr 0.0162 f_bond_d 0.0052
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2700 Nucleic Acid Atoms Solvent Atoms 335 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement STARANISO data scaling Coot model building autoPROC data reduction autoPROC data processing MrBUMP phasing