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Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikC with the HMA domain of Pikh-1 from rice (Oryza sativa)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7A8W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.12 M Monosaccharides (0.2M D-Glucose; 0.2M D-Mannose; 0.2M D-Galactose; 0.2M L-Fucose; 0.2M D-Xylose; 0.2M N-Acetyl-D-Glucosamine); 0.1 M Buffer system 1 (1 M Imidazole; MES monohydrate (acid)) pH 6.5; 50% v/v Precipitant mix 1 (40% v/v PEG 500; MME; 20 % w/v PEG 20000)
Crystal Properties Matthews coefficient Solvent content 2.68 54.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.351 α = 90 b = 83.121 β = 90 c = 107.842 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 2017-05-18 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) Rrim I (All) Rpim I (All) CC (Half) 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 2.3 107.84 96.4 0.061 0.064 0.018 1 22.7 13.1 25847
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 100 0.927 0.968 0.278 0.864 2.5 12
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7A8W 2.3 65.922 25793 1288 96.343 0.212 0.2101 0.2101 0.2559 0.2549 58.185
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] -0.996 -0.909 1.905
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.76 r_dihedral_angle_3_deg 16.562 r_dihedral_angle_4_deg 16.141 r_dihedral_angle_1_deg 7.807 r_lrange_it 4.624 r_lrange_other 4.601 r_scangle_it 3.118 r_scangle_other 3.115 r_mcangle_it 2.702 r_mcangle_other 2.702
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.76 r_dihedral_angle_3_deg 16.562 r_dihedral_angle_4_deg 16.141 r_dihedral_angle_1_deg 7.807 r_lrange_it 4.624 r_lrange_other 4.601 r_scangle_it 3.118 r_scangle_other 3.115 r_mcangle_it 2.702 r_mcangle_other 2.702 r_scbond_it 2.023 r_scbond_other 2.018 r_mcbond_it 1.825 r_mcbond_other 1.825 r_angle_refined_deg 1.488 r_angle_other_deg 1.18 r_nbd_refined 0.198 r_nbd_other 0.193 r_symmetry_nbd_other 0.18 r_symmetry_nbd_refined 0.18 r_nbtor_refined 0.15 r_symmetry_xyhbond_nbd_refined 0.149 r_xyhbond_nbd_refined 0.132 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.059 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3459 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data processing Aimless data scaling PHASER phasing Aimless data reduction