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Complex of blast (Magnaporthe oryzae) effector PBY2 with the engineered integrated HMA domain of Rwt7 from wheat
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 2.4 M ammonium sulfate, 0.1 M MES pH 6
Crystal Properties Matthews coefficient Solvent content 2.93 57.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.197 α = 90 b = 105.197 β = 90 c = 69.134 γ = 90
Symmetry Space Group P 43 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 EIGER2 XE 16M 2025-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.953709 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 1.8 74.5 100 0.147 0.148 0.022 1 22.2 45.9 36570
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 1.8 1.84 100 1.24 1.254 0.185 0.971 45.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.8 74.5 34669 1842 100 0.1744 0.17253 0.183 0.20974 0.2187 RANDOM 26.834
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] 0.99 0.99 -1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.611 r_dihedral_angle_1_deg 10.945 r_dihedral_angle_2_deg 7.924 r_long_range_B_refined 7.463 r_long_range_B_other 7.462 r_scangle_other 4.04 r_scbond_it 3.334 r_scbond_other 2.701 r_mcangle_other 2.041 r_mcangle_it 2.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.611 r_dihedral_angle_1_deg 10.945 r_dihedral_angle_2_deg 7.924 r_long_range_B_refined 7.463 r_long_range_B_other 7.462 r_scangle_other 4.04 r_scbond_it 3.334 r_scbond_other 2.701 r_mcangle_other 2.041 r_mcangle_it 2.04 r_angle_refined_deg 1.893 r_mcbond_it 1.398 r_mcbond_other 1.392 r_angle_other_deg 0.62 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2130 Nucleic Acid Atoms Solvent Atoms 305 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction PHASER phasing PDB_EXTRACT data extraction