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Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikE with the HMA domain of Pikm-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 0.1M Amino acids (0.2M L-Na-Glutamate; 0.2M Alanine (racemic); 0.2M Glycine; 0.2M Lysine HCl (racemic); 0.2M Serine (racemic)); 0.1M Buffer system 2 (1M sodium HEPES, MOPS (acid)) pH 7.5; 50% v/v Precipitant mix 2 (40% v/v Ethylene glycol; 20 % w/v PEG 8000)
Crystal Properties Matthews coefficient Solvent content 2.04 39.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.023 α = 90 b = 54.345 β = 90.53 c = 48.493 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 2015-11-28 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) 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 1.3 23.7 99.4 0.071 12.9 7.6 38170
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 1.3 1.32
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 1.3 23.7 36190 1959 99.33 0.14296 0.14087 0.1401 0.17854 0.1791 RANDOM 21.377
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] 1.66 0.42 -1.03 -0.65
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 32.198 r_dihedral_angle_2_deg 31.486 r_sphericity_bonded 17.551 r_dihedral_angle_4_deg 16.307 r_dihedral_angle_3_deg 12.451 r_dihedral_angle_1_deg 6.557 r_long_range_B_refined 5.736 r_long_range_B_other 4.38 r_rigid_bond_restr 3.053 r_mcangle_it 3.008
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 32.198 r_dihedral_angle_2_deg 31.486 r_sphericity_bonded 17.551 r_dihedral_angle_4_deg 16.307 r_dihedral_angle_3_deg 12.451 r_dihedral_angle_1_deg 6.557 r_long_range_B_refined 5.736 r_long_range_B_other 4.38 r_rigid_bond_restr 3.053 r_mcangle_it 3.008 r_mcangle_other 3.008 r_scangle_other 2.998 r_scbond_it 2.558 r_scbond_other 2.556 r_mcbond_it 2.304 r_mcbond_other 2.301 r_angle_refined_deg 1.925 r_angle_other_deg 1.014 r_chiral_restr 0.117 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 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 1352 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing