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Crystal structure of the soluble domain of TrwG Type IV secretion machinery from Bartonella grahamii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JF8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 289 BagrA.18388.b.B2.PW37127 at 19.5 mg/mL against PACT condition B11, 0.2 M CaCl2, 0.1 M MES pH 6.0, 20% PEG 6000 supplemented with 20% glycerol as cryo-protectant, crystal tracking ID 248166b11, unique puck ID ngo7-6, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.16 43.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.95 α = 90 b = 87.65 β = 90 c = 191.83 γ = 90
Symmetry Space Group P 21 21 21
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 2013-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97856 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 2 50 99.1 0.08 15.35 71950 -3 30.553
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 2 2.05 100 0.505 3.61
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4JF8 2 50 71949 3620 99.11 0.1976 0.1953 0.204 0.2404 0.2483 RANDOM 31.9757
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] -0.49 2.33 -1.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.129 r_dihedral_angle_4_deg 20.426 r_dihedral_angle_3_deg 13.375 r_dihedral_angle_1_deg 6.538 r_mcangle_it 1.933 r_angle_refined_deg 1.495 r_mcbond_it 1.146 r_mcbond_other 1.145 r_angle_other_deg 0.786 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.129 r_dihedral_angle_4_deg 20.426 r_dihedral_angle_3_deg 13.375 r_dihedral_angle_1_deg 6.538 r_mcangle_it 1.933 r_angle_refined_deg 1.495 r_mcbond_it 1.146 r_mcbond_other 1.145 r_angle_other_deg 0.786 r_chiral_restr 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6640 Nucleic Acid Atoms Solvent Atoms 612 Heterogen Atoms 4
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction