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Complex of blast (Magnaporthe oryzae) effector PWT7 with the 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, HANGING DROP 293 0.2 M ammonium sulfate, 0.1 M sodium acetate pH 4.2, 16% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.65 53.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.915 α = 90 b = 73.609 β = 90 c = 127.544 γ = 90
Symmetry Space Group P 2 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 EIGER2 XE 16M 2024-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.953738 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 1.6 63.85 100 0.053 0.054 0.011 1 32.7 27 50590
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 1.6 1.63 100 1.043 1.063 0.201 0.961 27.9
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 1.6 63.85 48044 2484 100 0.16298 0.16124 0.1696 0.19766 0.2028 RANDOM 37.751
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] 0.38 2.7 -3.08
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 19.559 r_long_range_B_other 18.604 r_dihedral_angle_3_deg 13.084 r_dihedral_angle_2_deg 9.813 r_scangle_other 8.485 r_scbond_it 6.703 r_mcangle_other 6.602 r_mcangle_it 6.596 r_dihedral_angle_1_deg 6.59 r_scbond_other 5.807
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 19.559 r_long_range_B_other 18.604 r_dihedral_angle_3_deg 13.084 r_dihedral_angle_2_deg 9.813 r_scangle_other 8.485 r_scbond_it 6.703 r_mcangle_other 6.602 r_mcangle_it 6.596 r_dihedral_angle_1_deg 6.59 r_scbond_other 5.807 r_mcbond_it 4.467 r_mcbond_other 4.466 r_rigid_bond_restr 4.267 r_angle_refined_deg 1.776 r_angle_other_deg 0.581 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 2413 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction PHASER phasing PDB_EXTRACT data extraction