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The structure of S. aureus alpha-hemolysin in complex with a bicyclic peptide inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YHD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 290.15 Protein buffer:30mM HEPES pH 7.6, 150mM NaCl and 1mM TCEP.
Crystallisation buffer: 0.2M calcium chloride dihydrate, 0.1M sodium acetate and 20% (w/v) PEG6000.
Crystal Properties Matthews coefficient Solvent content 2.91 57.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.839 α = 71.15 b = 59.041 β = 86.36 c = 72.473 γ = 70.58
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 EIGER2 XE 16M 2023-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.4 50.77 98.7 0.093 0.11 0.057 0.995 8.2 3.6 30721
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 98 0.535 0.626 0.323 0.858 3.7
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 MOLECULAR REPLACEMENT THROUGHOUT 2.4 50.77 29166 1522 98.58 0.16414 0.16148 0.1672 0.21467 0.2177 RANDOM 34.978
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] 2.76 3.44 -1.72 0.23 -0.7 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.3 r_long_range_B_refined 7.791 r_long_range_B_other 7.791 r_dihedral_angle_2_deg 7.374 r_dihedral_angle_1_deg 7.219 r_scangle_other 5.868 r_mcangle_it 4.156 r_mcangle_other 4.156 r_scbond_it 3.678 r_scbond_other 3.678
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.3 r_long_range_B_refined 7.791 r_long_range_B_other 7.791 r_dihedral_angle_2_deg 7.374 r_dihedral_angle_1_deg 7.219 r_scangle_other 5.868 r_mcangle_it 4.156 r_mcangle_other 4.156 r_scbond_it 3.678 r_scbond_other 3.678 r_mcbond_it 2.708 r_mcbond_other 2.699 r_angle_refined_deg 1.502 r_angle_other_deg 0.53 r_chiral_restr 0.07 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 4760 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction PHASER phasing PDB_EXTRACT data extraction