4NOO

Molecular mechanism for self-protection against type VI secretion system in Vibrio cholerae


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.628915% (m/v) PEG8000, 0.1M Sodium Cacodylate pH5.6, 0.2M Mg acetate, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.9758.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.502α = 90
b = 116.034β = 94.05
c = 68.225γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2013-05-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBSRF BEAMLINE 3W1A0.9789BSRF3W1A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.329.599.920.072287.73436934369
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.341000.4224.97.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.329.53436934369182299.920.188680.186290.23441RANDOM20.487
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]
0.57-0.05-1.130.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.747
r_dihedral_angle_4_deg18.632
r_dihedral_angle_3_deg13.67
r_dihedral_angle_1_deg5.389
r_angle_other_deg3.597
r_angle_refined_deg1.278
r_chiral_restr0.074
r_bond_refined_d0.01
r_gen_planes_other0.008
r_gen_planes_refined0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.747
r_dihedral_angle_4_deg18.632
r_dihedral_angle_3_deg13.67
r_dihedral_angle_1_deg5.389
r_angle_other_deg3.597
r_angle_refined_deg1.278
r_chiral_restr0.074
r_bond_refined_d0.01
r_gen_planes_other0.008
r_gen_planes_refined0.005
r_bond_other_d
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4734
Nucleic Acid Atoms
Solvent Atoms525
Heterogen Atoms

Software

Software
Software NamePurpose
ADSCdata collection
PHENIXmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing