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Truncated derivative of the C-terminal domain of the TssA component of the type VI secretion system from Burkholderia cenocepacia
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6H8F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 0.18 M tri-ammonium citrate, 20% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.58 52.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.28 α = 90 b = 65.28 β = 90 c = 66.14 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 PIXEL DECTRIS PILATUS 6M-F 2014-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97943 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.35 42.97 99.9 0.094 0.037 17.1 8.5 6747
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.41 0.713 0.286 492
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6H8F 2.35 42.97 6372 357 99.85 0.19543 0.19307 0.23694 0.2266 RANDOM 45.245
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] 1.48 0.74 1.48 -4.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.997 r_dihedral_angle_4_deg 17.084 r_dihedral_angle_3_deg 15.269 r_long_range_B_refined 8.73 r_long_range_B_other 8.728 r_scangle_other 6.796 r_dihedral_angle_1_deg 6.202 r_mcangle_it 4.916 r_mcangle_other 4.911 r_scbond_it 4.261
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.997 r_dihedral_angle_4_deg 17.084 r_dihedral_angle_3_deg 15.269 r_long_range_B_refined 8.73 r_long_range_B_other 8.728 r_scangle_other 6.796 r_dihedral_angle_1_deg 6.202 r_mcangle_it 4.916 r_mcangle_other 4.911 r_scbond_it 4.261 r_scbond_other 4.243 r_mcbond_it 3.109 r_mcbond_other 3.109 r_angle_refined_deg 1.432 r_angle_other_deg 0.972 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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 897 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing