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Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikF with an engineered HMA domain of Pikp-1 (Pikp-SNK-EKE) from rice (Oryza sativa)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A6W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 NULL
Crystal Properties Matthews coefficient Solvent content 2.5 50.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.381 α = 90 b = 80.782 β = 90 c = 103.804 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 6M 2018-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 2.2 103.8 97.4 0.097 0.105 0.038 0.998 11.5 6.9 28553
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 2.2 2.27 99 0.751 0.814 0.302 0.844 6.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 5A6W 2.2 63.83 27072 1437 96.75 0.234 0.2313 0.2336 0.2855 0.2854 RANDOM 42.021
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] -2.79 3.51 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.693 r_dihedral_angle_4_deg 19.846 r_dihedral_angle_3_deg 17.388 r_dihedral_angle_1_deg 8.176 r_angle_refined_deg 1.597 r_angle_other_deg 1.192 r_chiral_restr 0.063 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.693 r_dihedral_angle_4_deg 19.846 r_dihedral_angle_3_deg 17.388 r_dihedral_angle_1_deg 8.176 r_angle_refined_deg 1.597 r_angle_other_deg 1.192 r_chiral_restr 0.063 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3526 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PDB_EXTRACT data extraction PHASER phasing