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Crystal structure of the type VI effector-immunity complex (Tae4-Tai4) from Agrobacterium tumefaciens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BI8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 35 % PEG 400, 0.05 M Tris pH 8.5, 0.05 M sodium sulfate, 0.05 M lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.46 49.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.025 α = 90 b = 72.025 β = 90 c = 194.348 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX225-HS 2015-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.0000 SPring-8 BL32XU
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 1.9 97.18 99.6 0.067 0.07 0.022 0.999 15 10.1 44633
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 1.9 1.94 96.3 1.431 1.538 0.544 0.528 7.3
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 4BI8 1.9 62.38 42275 2278 99.54 0.19142 0.19027 0.1981 0.21252 0.2153 RANDOM 47.589
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] 0.95 0.47 0.95 -3.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.819 r_dihedral_angle_1_deg 20.979 r_dihedral_angle_4_deg 18.281 r_dihedral_angle_3_deg 15.66 r_long_range_B_other 9.235 r_long_range_B_refined 9.229 r_scangle_other 6.79 r_mcangle_other 5.63 r_mcangle_it 5.629 r_scbond_it 4.908
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.819 r_dihedral_angle_1_deg 20.979 r_dihedral_angle_4_deg 18.281 r_dihedral_angle_3_deg 15.66 r_long_range_B_other 9.235 r_long_range_B_refined 9.229 r_scangle_other 6.79 r_mcangle_other 5.63 r_mcangle_it 5.629 r_scbond_it 4.908 r_scbond_other 4.906 r_mcbond_it 4.413 r_mcbond_other 4.411 r_angle_refined_deg 1.572 r_angle_other_deg 1.4 r_chiral_restr 0.077 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_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 4036 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction DIALS data reduction MOLREP phasing