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Crystal structure of the Makes Caterpillars Floppy (MCF)-Like effector of Vibrio vulnificus MO6-24/O
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6II6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 12% PEG 3000, 0.1M Na2HPO4/citric acid (pH 4.2), 0.4M NaCl, 10% glycerol
Crystal Properties Matthews coefficient Solvent content 2.46 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.64 α = 90 b = 78.64 β = 90 c = 450.008 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 270 2018-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.9793 PAL/PLS 7A (6B, 6C1)
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 2.36 50 97.3 6.1 5 60806
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 2.36 2.4 0.643 0.273 0.77
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 6II6 2.36 50 59323 3193 97.28 0.18517 0.18242 0.191 0.23662 0.2405 RANDOM 39.146
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] 0.11 0.06 0.11 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.163 r_dihedral_angle_4_deg 18.791 r_dihedral_angle_3_deg 15.994 r_long_range_B_refined 9.411 r_long_range_B_other 9.41 r_dihedral_angle_1_deg 7.167 r_scangle_other 6.557 r_mcangle_it 5.681 r_mcangle_other 5.68 r_scbond_it 4.356
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.163 r_dihedral_angle_4_deg 18.791 r_dihedral_angle_3_deg 15.994 r_long_range_B_refined 9.411 r_long_range_B_other 9.41 r_dihedral_angle_1_deg 7.167 r_scangle_other 6.557 r_mcangle_it 5.681 r_mcangle_other 5.68 r_scbond_it 4.356 r_scbond_other 4.354 r_mcbond_it 3.631 r_mcbond_other 3.63 r_angle_refined_deg 1.436 r_angle_other_deg 0.83 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.002 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 9567 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing Coot model building REFMAC refinement