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Complex of blast (Magnaporthe oryzae) effector 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 0.2 M ammonium sulfate, 0.1 M sodium acetate pH 4, 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.21 61.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.075 α = 90 b = 90.075 β = 90 c = 88.228 γ = 120
Symmetry Space Group P 31 1 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 2024-10-06 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 2.6 88.23 100 0.107 0.108 0.017 1 24.7 41.5 12793
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 2.6 2.72 100 2.442 2.471 0.376 0.888 42.9
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 2.6 78.13 12044 723 99.99 0.19219 0.188 0.1952 0.26168 0.2649 RANDOM 93.148
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] 1.92 0.96 1.92 -6.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.744 r_dihedral_angle_2_deg 14.67 r_long_range_B_refined 12.315 r_long_range_B_other 12.314 r_scangle_other 11.13 r_mcangle_other 9.341 r_mcangle_it 9.338 r_dihedral_angle_1_deg 8.782 r_scbond_it 8.285 r_scbond_other 8.254
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.744 r_dihedral_angle_2_deg 14.67 r_long_range_B_refined 12.315 r_long_range_B_other 12.314 r_scangle_other 11.13 r_mcangle_other 9.341 r_mcangle_it 9.338 r_dihedral_angle_1_deg 8.782 r_scbond_it 8.285 r_scbond_other 8.254 r_mcbond_other 7.084 r_mcbond_it 7.08 r_angle_refined_deg 2.772 r_angle_other_deg 0.853 r_chiral_restr 0.107 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 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 2056 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction PHASER phasing PDB_EXTRACT data extraction