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Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikD with the HMA domain of Pikp1 from rice (Oryza sativa)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A6P PDB ENTRY 5A6P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 2M AMMONIUM SULPHATE, 0.1M CHES PH 9 AND 20% PEG335
Crystal Properties Matthews coefficient Solvent content 2.38 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.41 α = 90 b = 118.41 β = 90 c = 35.81 γ = 90
Symmetry Space Group P 41 21 2
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 PILATUS 6M 2014-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 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 1.6 39.47 100 0.05 32.3 17.7 32549 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.64 100 0.65 4.7 17.4
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 PDB ENTRY 5A6P 1.6 39.47 32549 1712 99.96 0.17908 0.17763 0.1874 0.20544 0.2143 RANDOM 31.154
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] 0.17 0.17 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.929 r_dihedral_angle_4_deg 15.629 r_dihedral_angle_3_deg 12.497 r_dihedral_angle_1_deg 5.834 r_mcangle_it 2.631 r_scbond_it 2.25 r_mcbond_it 1.634 r_mcbond_other 1.618 r_angle_refined_deg 1.567 r_angle_other_deg 0.729
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.929 r_dihedral_angle_4_deg 15.629 r_dihedral_angle_3_deg 12.497 r_dihedral_angle_1_deg 5.834 r_mcangle_it 2.631 r_scbond_it 2.25 r_mcbond_it 1.634 r_mcbond_other 1.618 r_angle_refined_deg 1.567 r_angle_other_deg 0.729 r_chiral_restr 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1736 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling