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Crystal structure of the homodimeric AvrM14-B Nudix hydrolase effector from Melampsora lini
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8DP9 AvrM14-B Monomer
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 1.8 M Ammonium sulphate
0.1 M Sodium acetate pH 4.2 - 4.4
0.1 M Magnesium chloride
Crystal Properties Matthews coefficient Solvent content 4.8 74.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.663 α = 90 b = 79.663 β = 90 c = 201.317 γ = 90
Symmetry Space Group P 41 21 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 EIGER X 16M 2019-09-14 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 1.839 35.63 99.54 0.08854 0.09289 0.02773 0.999 16.34 11 57219 35.82
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.839 1.905 96.36 0.484 0.84 10.8
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 AvrM14-B Monomer 1.84 35.63 1.34 57038 2832 99.56 0.1912 0.1896 0.1895 0.2215 0.2212 48.37
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 16.5985 f_angle_d 0.959 f_chiral_restr 0.066 f_bond_d 0.0097 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2123 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 15
Software Software Software Name Purpose PHENIX refinement Coot model building PHENIX model building XDS data reduction Aimless data scaling PHASER phasing