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Crystal structure of gatekeeper of type III secretion system in Bordetella BopN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.16M Calcium acetate, 0.08M sodium cacodylate, 14.4% (w/v) PEG 8000, 20% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 3.14 60.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.859 α = 90 b = 84.859 β = 90 c = 102.565 γ = 90
Symmetry Space Group P 42 2 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 PILATUS 6M 2015-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.987 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.95 43.93 97.5 0.1 0.99 18.7 8.88 26601 36.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 0.127 0.73 1.75
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION AB INITIO PHASING THROUGHOUT 1.95 43.93 26586 1400 99.91 0.18103 0.17968 0.1893 0.20709 0.2164 RANDOM 46.007
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 -0.39 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.307 r_dihedral_angle_3_deg 12.558 r_dihedral_angle_4_deg 11.852 r_long_range_B_other 10.376 r_long_range_B_refined 10.369 r_scangle_other 9.685 r_scbond_it 7.562 r_scbond_other 7.559 r_mcangle_it 5.451 r_mcangle_other 5.449
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.307 r_dihedral_angle_3_deg 12.558 r_dihedral_angle_4_deg 11.852 r_long_range_B_other 10.376 r_long_range_B_refined 10.369 r_scangle_other 9.685 r_scbond_it 7.562 r_scbond_other 7.559 r_mcangle_it 5.451 r_mcangle_other 5.449 r_mcbond_it 4.779 r_mcbond_other 4.77 r_dihedral_angle_1_deg 3.825 r_angle_other_deg 0.997 r_angle_refined_deg 0.858 r_chiral_restr 0.046 r_bond_refined_d 0.004 r_gen_planes_refined 0.002 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 2067 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling Arcimboldo phasing