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Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikD with the 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 6.5 293 0.12M Alcohols (0.2M 1,6-Hexanediol; 0.2M 1-Butanol; 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol); 0.1M Buffer system 1 (1M Imidazole; MES monohydrate (acid)) pH 6.5; 50% v/v Precipitant mix 4 (25%v/v MPD; 25%v/v PEG 1000; 25%v/v PEG3350)
Crystal Properties Matthews coefficient Solvent content 2.04 39.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.5 α = 90 b = 66.261 β = 113.32 c = 45.739 γ = 90
Symmetry Space Group P 1 21 1
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 2016-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.35 42 99.8 0.061 13.4 6.6 48646
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.37
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5A6W 1.35 42 46253 2368 99.78 0.1447 0.14267 0.1544 0.18355 0.1876 RANDOM 23.14
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] 3.32 0.38 -2.72 -0.68
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 33.192 r_dihedral_angle_2_deg 32.18 r_sphericity_bonded 18.879 r_dihedral_angle_4_deg 15.679 r_dihedral_angle_3_deg 13.463 r_dihedral_angle_1_deg 5.993 r_long_range_B_refined 4.932 r_long_range_B_other 4.389 r_scangle_other 3.686 r_scbond_it 3.302
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 33.192 r_dihedral_angle_2_deg 32.18 r_sphericity_bonded 18.879 r_dihedral_angle_4_deg 15.679 r_dihedral_angle_3_deg 13.463 r_dihedral_angle_1_deg 5.993 r_long_range_B_refined 4.932 r_long_range_B_other 4.389 r_scangle_other 3.686 r_scbond_it 3.302 r_scbond_other 3.271 r_rigid_bond_restr 3.128 r_mcangle_other 2.778 r_mcangle_it 2.768 r_mcbond_it 2.182 r_mcbond_other 2.148 r_angle_refined_deg 1.919 r_angle_other_deg 1.016 r_chiral_restr 0.117 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1759 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing