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Complex of rice blast (Magnaporthe oryzae) effector protein AVR-Pia with the HMA domain of OsHPP09 from rice (Oryza sativa)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold experimental model PDB 6Q76
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1 M MES pH 6.5, 0.2 M ammonium sulphate, 20% (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.911 57.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.665 α = 90 b = 93.665 β = 90 c = 72.873 γ = 120
Symmetry Space Group P 61 2 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 PILATUS3 6M 2023-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9655 ESRF MASSIF-1
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 1.65 46.83 99.8 0.037 0.044 0.025 0.999 19.2 5.6 23168
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 1.65 1.68 100 0.874 1.059 0.592 0.837 1.9 5.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.65 46.83 23139 1151 99.673 0.177 0.176 0.1748 0.2021 0.2007 36.032
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] 0.799 0.399 0.799 -2.591
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.422 r_dihedral_angle_3_deg 14.017 r_lrange_it 10.854 r_lrange_other 10.81 r_scangle_it 8.683 r_scangle_other 8.664 r_dihedral_angle_1_deg 6.788 r_scbond_it 6.001 r_scbond_other 5.993 r_mcangle_it 4.871
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.422 r_dihedral_angle_3_deg 14.017 r_lrange_it 10.854 r_lrange_other 10.81 r_scangle_it 8.683 r_scangle_other 8.664 r_dihedral_angle_1_deg 6.788 r_scbond_it 6.001 r_scbond_other 5.993 r_mcangle_it 4.871 r_mcangle_other 4.868 r_dihedral_angle_2_deg 4.706 r_mcbond_it 3.54 r_mcbond_other 3.538 r_angle_refined_deg 2.243 r_angle_other_deg 0.768 r_nbd_other 0.347 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.211 r_symmetry_nbd_other 0.21 r_symmetry_nbd_refined 0.184 r_nbtor_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.167 r_chiral_restr 0.118 r_symmetry_nbtor_other 0.094 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_chiral_restr_other 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1053 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 10
Software Software Software Name Purpose EDNA data collection XDS data reduction PHASER phasing Aimless data scaling REFMAC refinement