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Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikE 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 0.06M Divalents (0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dihydrate); 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 2.58 52.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.196 α = 90 b = 80.177 β = 90 c = 105.627 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 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 1.9 46.29 100 0.1 14.5 12 45720
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 1.9 1.94
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 1.9 46.29 43475 2178 99.89 0.20954 0.20876 0.2168 0.22443 0.229 RANDOM 36.046
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] -2.96 4.84 -1.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.236 r_dihedral_angle_3_deg 14.204 r_dihedral_angle_4_deg 9.889 r_long_range_B_refined 7.758 r_long_range_B_other 7.723 r_dihedral_angle_1_deg 6.235 r_scangle_other 5.667 r_mcangle_it 4.225 r_mcangle_other 4.225 r_scbond_it 3.713
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.236 r_dihedral_angle_3_deg 14.204 r_dihedral_angle_4_deg 9.889 r_long_range_B_refined 7.758 r_long_range_B_other 7.723 r_dihedral_angle_1_deg 6.235 r_scangle_other 5.667 r_mcangle_it 4.225 r_mcangle_other 4.225 r_scbond_it 3.713 r_scbond_other 3.707 r_mcbond_it 2.934 r_mcbond_other 2.931 r_angle_refined_deg 1.614 r_angle_other_deg 0.893 r_chiral_restr 0.091 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 3436 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing