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Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikA 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 0.12M 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 2 (1M sodium HEPES, MOPS (acid)) pH 7.5; 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 1.91 35.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.07 α = 90 b = 54.44 β = 104.43 c = 46.64 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 34.76 99.3 0.043 21.5 7.8 33854
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 1.33
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5A6W 1.3 34.76 33854 1720 99.25 0.12719 0.12542 0.16191 0.1769 RANDOM 22.458
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] -1.68 0.67 -0.06 1.24
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 33.372 r_dihedral_angle_2_deg 32.269 r_dihedral_angle_4_deg 14.647 r_sphericity_bonded 14.304 r_dihedral_angle_3_deg 12.12 r_dihedral_angle_1_deg 6.968 r_long_range_B_refined 5.667 r_long_range_B_other 5.665 r_scangle_other 4.994 r_scbond_it 3.996
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 33.372 r_dihedral_angle_2_deg 32.269 r_dihedral_angle_4_deg 14.647 r_sphericity_bonded 14.304 r_dihedral_angle_3_deg 12.12 r_dihedral_angle_1_deg 6.968 r_long_range_B_refined 5.667 r_long_range_B_other 5.665 r_scangle_other 4.994 r_scbond_it 3.996 r_scbond_other 3.991 r_mcangle_it 3.522 r_mcangle_other 3.52 r_rigid_bond_restr 2.83 r_mcbond_it 2.759 r_mcbond_other 2.742 r_angle_refined_deg 1.775 r_angle_other_deg 0.984 r_chiral_restr 0.115 r_bond_refined_d 0.017 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 1239 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing