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Crystal structure of the soluble domain of a Type IV secretion system protein VirB8 from Bartonella quintana Toulouse
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KZ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 289 BaquA.18388.b.B2.PS01732 at 21 mg/mL against JCSG+ screen condition B9, 0.1 M Na citrate pH 5.0, 20% PEG 6000 with 20% ethylene glycol as cryo-protectant, crystal tracking ID 242024b9, unique puck ID fez5-10, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.94 36.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.73 α = 90 b = 60.73 β = 90 c = 87.86 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 CCD RAYONIX MX-300 2012-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 50 99.8 0.034 34.27 7.1 18788 18752 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 100 0.429 4.72
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 4kz1 1.7 43.97 17738 960 99.82 0.17581 0.17415 0.20713 0.2198 RANDOM 26.352
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] 0.23 0.23 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.852 r_sphericity_free 29.894 r_dihedral_angle_4_deg 21.886 r_dihedral_angle_3_deg 11.254 r_sphericity_bonded 7.926 r_dihedral_angle_1_deg 5.637 r_rigid_bond_restr 2.692 r_mcangle_it 1.92 r_scbond_it 1.602 r_angle_refined_deg 1.407
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.852 r_sphericity_free 29.894 r_dihedral_angle_4_deg 21.886 r_dihedral_angle_3_deg 11.254 r_sphericity_bonded 7.926 r_dihedral_angle_1_deg 5.637 r_rigid_bond_restr 2.692 r_mcangle_it 1.92 r_scbond_it 1.602 r_angle_refined_deg 1.407 r_mcbond_it 1.188 r_mcbond_other 1.171 r_angle_other_deg 0.755 r_chiral_restr 0.093 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1120 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction