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Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikD 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 8.5 293 0.12M Ethylene glycols (0.3M Diethylene glycol; 0.3M Triethylene-glycol; 0.3M Tetraethylene glycol; 0.3M Pentaethylene glycol); 0.1M Buffer system 3 (1M Tris (base); BICINE) pH 8.5; 50% v/v Precipitant mix 2 (40% v/v Ethylene glycol; 20 % w/v PEG 8000)
Crystal Properties Matthews coefficient Solvent content 2.16 43.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.09 α = 90 b = 87.13 β = 90 c = 103.84 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 2016-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.91680 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 1.2 29.04 98.5 0.049 21.7 11.9 104301
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 1.2 1.23
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 1.2 29.04 99199 5033 98.33 0.15025 0.14852 0.1582 0.18435 0.1885 RANDOM 22.92
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] -1.35 -0.78 2.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.921 r_sphericity_free 30.754 r_dihedral_angle_4_deg 18.807 r_sphericity_bonded 16.539 r_dihedral_angle_3_deg 12.501 r_dihedral_angle_1_deg 6.473 r_long_range_B_refined 5.685 r_long_range_B_other 5.614 r_mcangle_it 4.323 r_mcangle_other 4.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.921 r_sphericity_free 30.754 r_dihedral_angle_4_deg 18.807 r_sphericity_bonded 16.539 r_dihedral_angle_3_deg 12.501 r_dihedral_angle_1_deg 6.473 r_long_range_B_refined 5.685 r_long_range_B_other 5.614 r_mcangle_it 4.323 r_mcangle_other 4.322 r_scangle_other 4.253 r_rigid_bond_restr 3.752 r_scbond_other 3.62 r_scbond_it 3.619 r_mcbond_other 3.327 r_mcbond_it 3.326 r_angle_refined_deg 1.902 r_angle_other_deg 1.112 r_chiral_restr 0.123 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 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 2573 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing