6H8E

Truncated derivative of the C-terminal domain of the TssA component of the type VI secretion system from Burkholderia cenocepacia


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6H8F 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2900.18 M tri-ammonium citrate, 20% (w/v) PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.5852.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.28α = 90
b = 65.28β = 90
c = 66.14γ = 120
Symmetry
Space GroupP 62

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97943DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
12.3542.9799.90.0940.03717.18.56747
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.352.410.7130.286492

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6H8F2.3542.97637235799.850.195430.193070.23694RANDOM45.245
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]
1.480.741.48-4.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.997
r_dihedral_angle_4_deg17.084
r_dihedral_angle_3_deg15.269
r_long_range_B_refined8.73
r_long_range_B_other8.728
r_scangle_other6.796
r_dihedral_angle_1_deg6.202
r_mcangle_it4.916
r_mcangle_other4.911
r_scbond_it4.261
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.997
r_dihedral_angle_4_deg17.084
r_dihedral_angle_3_deg15.269
r_long_range_B_refined8.73
r_long_range_B_other8.728
r_scangle_other6.796
r_dihedral_angle_1_deg6.202
r_mcangle_it4.916
r_mcangle_other4.911
r_scbond_it4.261
r_scbond_other4.243
r_mcbond_it3.109
r_mcbond_other3.109
r_angle_refined_deg1.432
r_angle_other_deg0.972
r_chiral_restr0.085
r_bond_refined_d0.013
r_gen_planes_refined0.006
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 Atoms897
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing