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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)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% PEG 3350, 0.1 M Bis-Tris-HCl (pH 5.5), and 2% Tacsimate (pH 4.0)
Crystal Properties Matthews coefficient Solvent content 2.41 48.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.293 α = 90 b = 117.523 β = 90 c = 186.348 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 S 6M 2017-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.9791 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.1 50 98.1 8.7 7 65267
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) Redundancy Number Unique Reflections (All) 1 2.1 2.14 0.612 0.228 0.889
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 THROUGHOUT 2.1 50 64463 3485 97.96 0.17783 0.17491 0.1899 0.23214 0.2446 RANDOM 30.946
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] 0.14 0.11 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.591 r_dihedral_angle_4_deg 18.912 r_dihedral_angle_3_deg 15.955 r_long_range_B_refined 8.067 r_long_range_B_other 8.045 r_dihedral_angle_1_deg 7.419 r_scangle_other 6.313 r_mcangle_it 4.398 r_mcangle_other 4.397 r_scbond_other 4.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.591 r_dihedral_angle_4_deg 18.912 r_dihedral_angle_3_deg 15.955 r_long_range_B_refined 8.067 r_long_range_B_other 8.045 r_dihedral_angle_1_deg 7.419 r_scangle_other 6.313 r_mcangle_it 4.398 r_mcangle_other 4.397 r_scbond_other 4.154 r_scbond_it 4.153 r_mcbond_it 2.923 r_mcbond_other 2.92 r_angle_refined_deg 1.376 r_angle_other_deg 0.77 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 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 7930 Nucleic Acid Atoms Solvent Atoms 581 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing Coot model building REFMAC refinement