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Structure of Salmonella TacT2 toxin bound to TacA2 antitoxin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FVJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 277 0.01M Magnessium chloride hexahydrate
0.05M MES monohydrate
1.8M Lithium sulfate monohydrate
Crystal Properties Matthews coefficient Solvent content 2.19 43.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.491 α = 100.57 b = 54.452 β = 97.73 c = 76.9 γ = 117
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 EIGER X 16M 2019-06-25 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 2.14 73.22 97.1 0.073 0.103 0.073 0.992 3.8 1.8 36519 29.113
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.14 2.18 92.2 0.726 0.514 1.2 1.8
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 5FVJ 2.14 46.66 34696 1795 97.07 0.2219 0.2197 0.224 0.2634 0.2677 RANDOM 37.95
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] 0.04 -0.01 0.05 -0.05 0.04 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.416 r_dihedral_angle_4_deg 17.916 r_dihedral_angle_3_deg 15.942 r_dihedral_angle_1_deg 6.554 r_angle_refined_deg 1.385 r_angle_other_deg 1.265 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.416 r_dihedral_angle_4_deg 17.916 r_dihedral_angle_3_deg 15.942 r_dihedral_angle_1_deg 6.554 r_angle_refined_deg 1.385 r_angle_other_deg 1.265 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4823 Nucleic Acid Atoms Solvent Atoms 321 Heterogen Atoms 103
Software Software Software Name Purpose REFMAC refinement xia2 data scaling PDB_EXTRACT data extraction xia2 data reduction PHASER phasing