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Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikC with an engineered HMA domain of Pikp-1 from rice (Oryza sativa)
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 0.12 M Monosaccharides (0.2M D-Glucose; 0.2M D-Mannose; 0.2M D-Galactose; 0.2M L-Fucose; 0.2M D-Xylose; 0.2M N-Acetyl-D-Glucosamine); 0.1 M Buffer system 2 (Sodium HEPES; MOPS (acid)) pH 7.5; 37.5% v/v Precipitant mix 4 (25% v/v MPD; 25% PEG
1000; 25% w/v PEG 3350)
Crystal Properties Matthews coefficient Solvent content 2.52 51.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.784 α = 90 b = 80.205 β = 90 c = 105.683 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 PILATUS3 6M 2017-05-18 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 2.15 46.17 99.9 0.053 0.055 0.015 1 23.9 13.2 31604
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 2.15 2.22 99.8 0.996 1.034 0.278 0.925 2.3 13.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5A6W 2.15 44.165 31548 1510 99.921 0.227 0.2241 0.221 0.2722 0.2692 63.54
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] -4.396 7.349 -2.953
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.047 r_dihedral_angle_4_deg 19.723 r_dihedral_angle_3_deg 16.847 r_lrange_other 9.148 r_lrange_it 9.146 r_dihedral_angle_1_deg 7.436 r_scangle_it 7.304 r_scangle_other 7.294 r_mcangle_it 6.291 r_mcangle_other 6.291
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.047 r_dihedral_angle_4_deg 19.723 r_dihedral_angle_3_deg 16.847 r_lrange_other 9.148 r_lrange_it 9.146 r_dihedral_angle_1_deg 7.436 r_scangle_it 7.304 r_scangle_other 7.294 r_mcangle_it 6.291 r_mcangle_other 6.291 r_scbond_it 5.117 r_scbond_other 5.114 r_mcbond_it 4.631 r_mcbond_other 4.623 r_angle_refined_deg 1.479 r_angle_other_deg 1.183 r_nbd_other 0.21 r_nbd_refined 0.198 r_symmetry_xyhbond_nbd_refined 0.192 r_symmetry_nbd_other 0.179 r_symmetry_nbd_refined 0.172 r_xyhbond_nbd_refined 0.159 r_nbtor_refined 0.152 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.056 r_symmetry_xyhbond_nbd_other 0.052 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3443 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms
Software Software Software Name Purpose XDS data processing Aimless data scaling PHASER phasing REFMAC refinement