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Crystal structure of a TrwG component of type IV secretion system protein from Bartonella birtlesii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BHM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 BabiA.18388.a.B2 PS01693 at 25.7 mg/mL against JCSG+ screen condition A3, 0.2 M citrate, 25% PEG 3350 with 20% ethylene glycol as cryo-protectant, unique puck ID vff2-9, crystal tracking ID 240866a3, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.75 29.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.15 α = 90 b = 72.15 β = 90 c = 47.44 γ = 120
Symmetry Space Group P 31 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 CCD ADSC QUANTUM 315r 2012-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.12709 SSRL BL7-1
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 1.35 50 99.7 0.038 34.59 8.3 31634 31529 -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 1.35 1.39 98.6 0.497 2.9
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 2bhm 1.35 50 29908 1588 99.64 0.15528 0.15426 0.1556 0.17514 0.1764 RANDOM 15.437
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] -0.39 -0.2 -0.39 1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.202 r_sphericity_free 26.635 r_dihedral_angle_4_deg 20.681 r_dihedral_angle_3_deg 10.988 r_sphericity_bonded 6.73 r_dihedral_angle_1_deg 5.754 r_rigid_bond_restr 1.769 r_mcangle_it 1.353 r_angle_refined_deg 1.304 r_scbond_it 1.207
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.202 r_sphericity_free 26.635 r_dihedral_angle_4_deg 20.681 r_dihedral_angle_3_deg 10.988 r_sphericity_bonded 6.73 r_dihedral_angle_1_deg 5.754 r_rigid_bond_restr 1.769 r_mcangle_it 1.353 r_angle_refined_deg 1.304 r_scbond_it 1.207 r_mcbond_it 0.814 r_mcbond_other 0.801 r_angle_other_deg 0.727 r_chiral_restr 0.078 r_bond_refined_d 0.009 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 1134 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 16
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection XDS data reduction