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Crystal structure of Phytophthora infestans effector AVRcap1b in complex with the ENTH domain of Nicotiana benthamiana NbTOL9a protein
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 7.5 294 NULL
Crystal Properties Matthews coefficient Solvent content 3.29 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.874 α = 90 b = 136.912 β = 90 c = 195.574 γ = 90
Symmetry Space Group P 21 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 2020-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 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 4.1 79.57 100 0.106 0.11 0.031 1 9.6 12.9 18772
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 4.1 4.49 100 2.126 2.208 0.595 0.518 13.6
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 4.1 79.57 17765 938 99.89 0.25005 0.24815 0.2479 0.28596 0.2819 RANDOM 274.406
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] -4 -2.54 6.53
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 36.25 r_long_range_B_other 36.249 r_mcangle_it 22.499 r_mcangle_other 22.498 r_scangle_other 21.963 r_dihedral_angle_3_deg 15.12 r_mcbond_it 13.647 r_mcbond_other 13.647 r_scbond_it 12.707 r_scbond_other 12.706
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 36.25 r_long_range_B_other 36.249 r_mcangle_it 22.499 r_mcangle_other 22.498 r_scangle_other 21.963 r_dihedral_angle_3_deg 15.12 r_mcbond_it 13.647 r_mcbond_other 13.647 r_scbond_it 12.707 r_scbond_other 12.706 r_dihedral_angle_1_deg 6.071 r_dihedral_angle_2_deg 5.278 r_angle_refined_deg 1.529 r_angle_other_deg 0.644 r_chiral_restr 0.088 r_gen_planes_refined 0.007 r_bond_refined_d 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.002 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 11839 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction PHASER phasing PDB_EXTRACT data extraction