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Complex of blast (Magnaporthe oryzae) effectors PWT7 and PBY2 with the engineered integrated HMA domain of Rmo2 from barley
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 0.1 M KBr, 30% (w/v) PEG2000 MME
Crystal Properties Matthews coefficient Solvent content 2.09 41.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.592 α = 90 b = 30.59 β = 93.02 c = 61.448 γ = 90
Symmetry Space Group P 1 21 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 EIGER2 XE 16M 2024-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.953727 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 1.4 61.36 100 0.056 0.058 0.016 1 19.8 13.5 41916
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 1.4 1.42 100 1.33 1.38 0.367 0.872 13.7
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 1.4 61.36 39752 2153 100 0.15306 0.15118 0.1508 0.18896 0.1888 RANDOM 26.85
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] 0.4 -0.58 -0.18 -0.16
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 12.033 r_dihedral_angle_3_deg 11.935 r_long_range_B_other 11.386 r_dihedral_angle_2_deg 8.162 r_dihedral_angle_1_deg 6.701 r_scangle_other 5.928 r_mcangle_it 4.335 r_mcangle_other 4.334 r_scbond_it 4.047 r_scbond_other 4.046
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 12.033 r_dihedral_angle_3_deg 11.935 r_long_range_B_other 11.386 r_dihedral_angle_2_deg 8.162 r_dihedral_angle_1_deg 6.701 r_scangle_other 5.928 r_mcangle_it 4.335 r_mcangle_other 4.334 r_scbond_it 4.047 r_scbond_other 4.046 r_rigid_bond_restr 3.021 r_mcbond_it 2.94 r_mcbond_other 2.939 r_angle_refined_deg 1.724 r_angle_other_deg 0.593 r_chiral_restr 0.085 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1715 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction PHASER phasing PDB_EXTRACT data extraction