6II6

Crystal structure of the Makes Caterpillars Floppy (MCF)-Like effector of Vibrio vulnificus MO6-24/O in complex with a human ADP-ribosylation factor 3 (ARF3)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29320% PEG 3350, 0.1 M Bis-Tris-HCl (pH 5.5), and 2% Tacsimate (pH 4.0)
Crystal Properties
Matthews coefficientSolvent content
2.4148.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.293α = 90
b = 117.523β = 90
c = 186.348γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2017-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.9791Photon FactoryBL-17A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.15098.18.7765267
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.140.6120.2280.889

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 DIFFRACTIONTHROUGHOUT2.15064463348597.960.177830.174910.23214RANDOM30.946
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]
0.140.11-0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.591
r_dihedral_angle_4_deg18.912
r_dihedral_angle_3_deg15.955
r_long_range_B_refined8.067
r_long_range_B_other8.045
r_dihedral_angle_1_deg7.419
r_scangle_other6.313
r_mcangle_it4.398
r_mcangle_other4.397
r_scbond_other4.154
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.591
r_dihedral_angle_4_deg18.912
r_dihedral_angle_3_deg15.955
r_long_range_B_refined8.067
r_long_range_B_other8.045
r_dihedral_angle_1_deg7.419
r_scangle_other6.313
r_mcangle_it4.398
r_mcangle_other4.397
r_scbond_other4.154
r_scbond_it4.153
r_mcbond_it2.923
r_mcbond_other2.92
r_angle_refined_deg1.376
r_angle_other_deg0.77
r_chiral_restr0.087
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms7930
Nucleic Acid Atoms
Solvent Atoms581
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Cootmodel building
REFMACrefinement