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Crystal structure of alpha-beta hydrolase (ABH) and Makes Caterpillars Floppy (MCF)-Like effectors of Vibrio vulnificus MO6-24/O
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6II6 6II6 AND 6IMP experimental model PDB 6IMP 6II6 AND 6IMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 22% PEG 4000, 0.1M Tris-HCl (pH 8.5), 0.2M Li2SO4
Crystal Properties Matthews coefficient Solvent content 2.61 52.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.215 α = 90 b = 108.593 β = 90 c = 334.737 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 CCD ADSC QUANTUM 315 2018-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.9794 PAL/PLS 5C (4A)
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 3.5 50 89.9 5.1 5.7 34303
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 3.5 3.56 1.509 0.581 0.562
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 AND 6IMP 3.5 49.6 29984 1514 77.5 0.28706 0.28503 0.2843 0.3274 0.3255 RANDOM 59.345
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] -0.6 0.84 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.085 r_dihedral_angle_4_deg 16.598 r_dihedral_angle_3_deg 16.164 r_long_range_B_refined 9.652 r_long_range_B_other 9.651 r_dihedral_angle_1_deg 8.166 r_mcangle_it 5.344 r_mcangle_other 5.344 r_scangle_other 4.413 r_mcbond_it 3.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.085 r_dihedral_angle_4_deg 16.598 r_dihedral_angle_3_deg 16.164 r_long_range_B_refined 9.652 r_long_range_B_other 9.651 r_dihedral_angle_1_deg 8.166 r_mcangle_it 5.344 r_mcangle_other 5.344 r_scangle_other 4.413 r_mcbond_it 3.067 r_mcbond_other 3.066 r_scbond_it 2.395 r_scbond_other 2.395 r_angle_refined_deg 1.195 r_angle_other_deg 0.808 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_bond_other_d 0.007 r_gen_planes_refined 0.007 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 17825 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing Coot model building REFMAC refinement