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Crystal structure of Dot/Icm T4SS effector Ceg10(C159S)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 289 0.1M sodium formate, 10% PEG3350, 15mM EDTA
Crystal Properties Matthews coefficient Solvent content 2.17 43.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.888 α = 91.4 b = 54.596 β = 91.11 c = 82.942 γ = 91.93
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 2023-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.97918 SSRF BL10U2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.79 50.89 95.9 0.995 5.5 2.9 81024
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.79 1.88 0.923
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.79 20 77109 3855 95.84 0.15612 0.1539 0.1654 0.1989 0.204 RANDOM 37.713
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] 1.96 0.23 2.78 -1.24 -0.44 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.095 r_dihedral_angle_1_deg 5.471 r_long_range_B_refined 5.023 r_long_range_B_other 4.927 r_dihedral_angle_2_deg 4.83 r_rigid_bond_restr 3.717 r_scangle_other 3.662 r_mcangle_it 3.423 r_mcangle_other 3.423 r_scbond_it 2.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.095 r_dihedral_angle_1_deg 5.471 r_long_range_B_refined 5.023 r_long_range_B_other 4.927 r_dihedral_angle_2_deg 4.83 r_rigid_bond_restr 3.717 r_scangle_other 3.662 r_mcangle_it 3.423 r_mcangle_other 3.423 r_scbond_it 2.53 r_scbond_other 2.53 r_mcbond_it 2.388 r_mcbond_other 2.385 r_angle_refined_deg 1.307 r_angle_other_deg 0.72 r_chiral_restr 0.07 r_gen_planes_other 0.008 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7138 Nucleic Acid Atoms Solvent Atoms 385 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling MOLREP phasing