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Crystal structure of VirB8-like OrfG central domain of Streptococcus thermophilus ICESt3; a putative assembly factor of a gram positive conjugative Type IV secretion system.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 Ammonium sulfate; 2M
Tris pH 8.5; 100 mM
Crystal Properties Matthews coefficient Solvent content 3.2 61.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.162 α = 90 b = 50.162 β = 90 c = 120.883 γ = 90
Symmetry Space Group P 41 21 2
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 9M 2019-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980 SOLEIL PROXIMA 2
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 1.75 46.331 100 0.027 0.028 0.006 1 67.5 25.1 16372 29.93
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 1.75 1.78 100 0.499 0.511 0.105 0.975 23.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 1.75 46.331 16309 835 99.951 0.2 0.1996 0.2032 0.2081 0.2104 Random 35.347
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] 0.701 0.701 -1.402
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 40.476 r_dihedral_angle_2_deg 34.206 r_dihedral_angle_3_deg 15.399 r_lrange_other 8.636 r_lrange_it 8.635 r_scangle_it 7.368 r_scangle_other 7.368 r_dihedral_angle_1_deg 6.107 r_scbond_other 5.303 r_scbond_it 5.281
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 40.476 r_dihedral_angle_2_deg 34.206 r_dihedral_angle_3_deg 15.399 r_lrange_other 8.636 r_lrange_it 8.635 r_scangle_it 7.368 r_scangle_other 7.368 r_dihedral_angle_1_deg 6.107 r_scbond_other 5.303 r_scbond_it 5.281 r_mcangle_other 4.545 r_mcangle_it 4.522 r_mcbond_other 3.596 r_mcbond_it 3.555 r_angle_other_deg 1.784 r_angle_refined_deg 1.635 r_symmetry_nbd_refined 0.387 r_nbd_refined 0.226 r_nbtor_refined 0.204 r_symmetry_xyhbond_nbd_refined 0.2 r_xyhbond_nbd_refined 0.191 r_symmetry_nbd_other 0.189 r_symmetry_xyhbond_nbd_other 0.176 r_nbd_other 0.175 r_symmetry_nbtor_other 0.1 r_chiral_restr 0.088 r_bond_other_d 0.021 r_bond_refined_d 0.014 r_gen_planes_other 0.005 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 842 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing