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Structure of the soluble AhlC of the tripartite alpha-pore forming toxin, AHL, from Aeromonas hydrophila.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SeMet AhlC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 290 0.2 M Sodium chloride
0.1 M Tris pH 8
20 % (w/v) PEG6000
Crystal Properties Matthews coefficient Solvent content 2.21 44.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.07 α = 90 b = 61.66 β = 92.01 c = 129.77 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS 6M 2014-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97626 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.62 46.74 99.7 0.074 0.058 11 3.4 31150 37.858
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.62 2.69 100 0.71 0.509 1.8 1.7
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 SeMet AhlC 2.62 46.74 29691 1448 99.62 0.27218 0.26909 0.2637 0.33432 0.3201 RANDOM 55.841
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] 1.58 -0.06 1.55 -3.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.977 r_dihedral_angle_4_deg 19.64 r_scbond_it 19.578 r_scbond_other 19.575 r_dihedral_angle_3_deg 18.468 r_scangle_other 16.218 r_long_range_B_refined 13.776 r_long_range_B_other 13.776 r_mcangle_it 7.179 r_mcangle_other 7.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.977 r_dihedral_angle_4_deg 19.64 r_scbond_it 19.578 r_scbond_other 19.575 r_dihedral_angle_3_deg 18.468 r_scangle_other 16.218 r_long_range_B_refined 13.776 r_long_range_B_other 13.776 r_mcangle_it 7.179 r_mcangle_other 7.178 r_dihedral_angle_1_deg 6.205 r_mcbond_it 4.934 r_mcbond_other 4.934 r_angle_refined_deg 1.475 r_angle_other_deg 0.955 r_chiral_restr 0.068 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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 6152 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing