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Crystal structure of the TIR domain from the grapevine disease resistance protein RUN1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6O0W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 0.2 M Lithium Sulfate, 0.1 M HEPES pH 7, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.67 53.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.435 α = 90 b = 41.471 β = 118.514 c = 77.232 γ = 90
Symmetry Space Group C 1 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 100 PIXEL DECTRIS EIGER X 16M 2019-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
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 1.89 33.93 99.48 0.062 0.074 0.04 0.997 12.06 3.4 34128 34.67
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 1.892 1.959 97.6 1.262 0.074 0.801 0.358 0.94 3.4
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6o0w 1.89 33.93 1.34 34118 1627 99.5 0.202 0.2008 0.2011 0.2263 0.2262 40.53
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 28.9654 f_angle_d 0.8072 f_chiral_restr 0.0521 f_bond_d 0.0079 f_plane_restr 0.0077
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2830 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 35
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing