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Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikD with a predicted ancestral HMA domain of Pik-1 from Oryza spp.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A6W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 NULL
Crystal Properties Matthews coefficient Solvent content 2.43 49.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.486 α = 90 b = 119.486 β = 90 c = 35.974 γ = 90
Symmetry Space Group P 41 21 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 2018-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9700 Diamond I03
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 1.32 59.81 96.3 0.068 0.07 0.018 0.999 16.7 14.6 59464
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 1.32 1.34 94.1 2.201 2.285 0.605 0.73 13.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 5A6W 1.32 59.81 56338 2981 96.1 0.1472 0.1452 0.1839 0.1923 RANDOM 21.866
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] 0.26 0.26 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.633 r_dihedral_angle_4_deg 16.11 r_dihedral_angle_3_deg 11.03 r_dihedral_angle_1_deg 6.659 r_rigid_bond_restr 2.289 r_angle_refined_deg 1.59 r_angle_other_deg 1.467 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.633 r_dihedral_angle_4_deg 16.11 r_dihedral_angle_3_deg 11.03 r_dihedral_angle_1_deg 6.659 r_rigid_bond_restr 2.289 r_angle_refined_deg 1.59 r_angle_other_deg 1.467 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1737 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement Aimless data reduction DIALS data reduction DIALS data scaling REFMAC phasing