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The Potato Late Blight pathogen (Phytophthora infestans) effector protein Pi04134 in complex with potato protein phosphatase type 1c (PP1c).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5INB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 0.2 M sodium fluoride, 0.1 M BIS-TRIS propose pH 8.5, 20 % PEG3350
Crystal Properties Matthews coefficient Solvent content 2.11 41.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.492 α = 84.35 b = 57.036 β = 86.49 c = 59.015 γ = 89.85
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 EIGER2 XE 16M 2019-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.91188 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.1 58.62 97.6 0.097 0.997 9.2 3.4 40927
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 0.527 0.84
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 5INB 2.1 58.62 38877 1979 97.36 0.20482 0.20246 0.2119 0.25141 0.2534 RANDOM 40.062
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] -2.54 -0.24 0.74 -0.82 -1.22 3.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.565 r_dihedral_angle_2_deg 9.926 r_dihedral_angle_1_deg 8.027 r_long_range_B_other 7.363 r_long_range_B_refined 7.345 r_scangle_other 4.266 r_mcangle_it 4.107 r_mcangle_other 4.107 r_scbond_it 2.669 r_scbond_other 2.668
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.565 r_dihedral_angle_2_deg 9.926 r_dihedral_angle_1_deg 8.027 r_long_range_B_other 7.363 r_long_range_B_refined 7.345 r_scangle_other 4.266 r_mcangle_it 4.107 r_mcangle_other 4.107 r_scbond_it 2.669 r_scbond_other 2.668 r_mcbond_it 2.505 r_mcbond_other 2.501 r_angle_refined_deg 1.659 r_angle_other_deg 0.547 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5889 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing