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Complex of Colletotrichum higginsianum effector protein ChEC108 with HMA domain 2 (HMA2) of HIPP6 from Arabidopsis thaliana.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AlphaFold2 model (accessed via ColabFold v.1.5.2) of HMA2 from HIPP6, specifically the sequence used for recombinant expression. in silico model AlphaFold AlphaFold2 model (accessed via ColabFold v.1.5.2) of ChEC108, specifically the sequence used for recombinant expression.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 16% PEG 6K, 0.1 M TRIS
Crystal Properties Matthews coefficient Solvent content 2.64 53.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.701 α = 70.36 b = 60.111 β = 89.72 c = 77.118 γ = 84.01
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 2023-05-23 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 2.2 72.61 99.4 0.114 0.124 0.049 0.996 9 6.1 32007
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 96.7 0.852 0.97 0.449 0.748 4.4
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 2.2 72.6 30335 1663 99.35 0.17434 0.17163 0.1798 0.22089 0.2242 RANDOM 45.612
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] 1.19 0.3 -0.57 1.81 -1.35 -3.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.087 r_long_range_B_refined 7.082 r_long_range_B_other 7.058 r_dihedral_angle_2_deg 7.018 r_dihedral_angle_1_deg 6.319 r_scangle_other 5.27 r_mcangle_it 3.672 r_mcangle_other 3.672 r_scbond_it 3.451 r_scbond_other 3.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.087 r_long_range_B_refined 7.082 r_long_range_B_other 7.058 r_dihedral_angle_2_deg 7.018 r_dihedral_angle_1_deg 6.319 r_scangle_other 5.27 r_mcangle_it 3.672 r_mcangle_other 3.672 r_scbond_it 3.451 r_scbond_other 3.45 r_mcbond_it 2.432 r_mcbond_other 2.432 r_angle_refined_deg 1.912 r_angle_other_deg 0.611 r_chiral_restr 0.087 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 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 4069 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction PHASER phasing PDB_EXTRACT data extraction