7YYG

Crystal structure of gatekeeper of type III secretion system in Bordetella BopN


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52770.16M Calcium acetate, 0.08M sodium cacodylate, 14.4% (w/v) PEG 8000, 20% (v/v) glycerol
Crystal Properties
Matthews coefficientSolvent content
3.1460.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.859α = 90
b = 84.859β = 90
c = 102.565γ = 90
Symmetry
Space GroupP 42 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.987BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.9543.9397.50.10.9918.78.882660136.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9520.1270.731.75

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONAB INITIO PHASINGTHROUGHOUT1.9543.9326586140099.910.181030.179680.20709RANDOM46.007
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]
-0.39-0.390.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.307
r_dihedral_angle_3_deg12.558
r_dihedral_angle_4_deg11.852
r_long_range_B_other10.376
r_long_range_B_refined10.369
r_scangle_other9.685
r_scbond_it7.562
r_scbond_other7.559
r_mcangle_it5.451
r_mcangle_other5.449
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.307
r_dihedral_angle_3_deg12.558
r_dihedral_angle_4_deg11.852
r_long_range_B_other10.376
r_long_range_B_refined10.369
r_scangle_other9.685
r_scbond_it7.562
r_scbond_other7.559
r_mcangle_it5.451
r_mcangle_other5.449
r_mcbond_it4.779
r_mcbond_other4.77
r_dihedral_angle_1_deg3.825
r_angle_other_deg0.997
r_angle_refined_deg0.858
r_chiral_restr0.046
r_bond_refined_d0.004
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms2067
Nucleic Acid Atoms
Solvent Atoms160
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
Arcimboldophasing