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Crystal structure of a double mutant of VirB8-like OrfG central and C-terminal domains of Streptococcus thermophilus ICESt3 (Gram positive conjugative type IV secretion system).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7PKW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Droplet: 0.3 ul [protein (33mg/ml) in 50 mM Tris pH 8.0 + 100 mM NaCl] + 0.3 ul [reservoir]
Reservoir: 50 ul [40% v/v PEG 300, 100 mM potassium phosphate citrate, pH 4.2]
Crystal Properties Matthews coefficient Solvent content 3.35 63.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.743 α = 90 b = 89.185 β = 112.314 c = 98.424 γ = 90
Symmetry Space Group C 1 2 1
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 4M 2022-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.967697 ESRF MASSIF-3
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 2.6 91.054 98.8 0.062 0.087 0.061 0.995 10.6 3.1 37215 50.28
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 2.6 2.72 99.8 0.665 0.933 0.653 0.682 1.8 3.3
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.6 91.054 37211 1819 98.564 0.204 0.2017 0.2563 0.2441 86.279
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] -2.736 -1.259 0.313 2.585
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.808 r_dihedral_angle_2_deg 16.183 r_lrange_it 15.484 r_lrange_other 15.484 r_dihedral_angle_6_deg 15.479 r_scangle_it 15.375 r_scangle_other 15.374 r_mcangle_it 12.904 r_mcangle_other 12.904 r_scbond_it 12.387
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.808 r_dihedral_angle_2_deg 16.183 r_lrange_it 15.484 r_lrange_other 15.484 r_dihedral_angle_6_deg 15.479 r_scangle_it 15.375 r_scangle_other 15.374 r_mcangle_it 12.904 r_mcangle_other 12.904 r_scbond_it 12.387 r_scbond_other 12.385 r_mcbond_it 10.727 r_mcbond_other 10.725 r_dihedral_angle_1_deg 8.758 r_angle_refined_deg 2.562 r_angle_other_deg 0.816 r_symmetry_xyhbond_nbd_refined 0.276 r_nbd_refined 0.212 r_symmetry_nbd_other 0.209 r_nbd_other 0.206 r_symmetry_nbd_refined 0.203 r_nbtor_refined 0.197 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.112 r_symmetry_xyhbond_nbd_other 0.1 r_symmetry_nbtor_other 0.095 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_ext_dist_refined_b 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5912 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction pointless data scaling MOLREP phasing