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Complex between S. aureus aureolysin and wt IMPI.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BQB 1BQB, 3SSB experimental model PDB 3SSB 1BQB, 3SSB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 Best crystals of aureolysin in complex with either IMPI variant were obtained at 20 degrees with protein solutions consisting of 5 mg/mL of aureolysin and 2.9 mg/mL of IMPI (peptidase:inhibitor molar ratio of 1:2.5) in 50 mM Tris-HCl, 150 mM sodium chloride, 1.6 mM calcium chloride, 8.3 microM zinc chloride, pH 8.0, which was mixed with reservoir solution comprising 0.1 M Bis-Tris, 25% (w/v) PEG 3350, pH 5.5.
Crystal Properties Matthews coefficient Solvent content 2.33 47.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.14 α = 90 b = 68.14 β = 90 c = 166.18 γ = 90
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 2020-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9793 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.85 52.7 100 0.149 0.042 0.999 14.7 13.6 64323 42.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.96 2.772 0.788 0.63 1.9
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1BQB, 3SSB 1.85 52.689 64322 724 99.966 0.165 0.1644 0.2186 0.2259 38.072
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] 11.211 11.211 -22.422
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.58 r_dihedral_angle_3_deg 16.598 r_dihedral_angle_4_deg 12.465 r_dihedral_angle_1_deg 7.262 r_lrange_it 5.055 r_scangle_it 2.802 r_mcangle_it 2.54 r_scbond_it 1.974 r_mcbond_it 1.787 r_angle_refined_deg 1.644
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.58 r_dihedral_angle_3_deg 16.598 r_dihedral_angle_4_deg 12.465 r_dihedral_angle_1_deg 7.262 r_lrange_it 5.055 r_scangle_it 2.802 r_mcangle_it 2.54 r_scbond_it 1.974 r_mcbond_it 1.787 r_angle_refined_deg 1.644 r_nbtor_refined 0.276 r_symmetry_nbd_refined 0.181 r_nbd_refined 0.159 r_chiral_restr 0.143 r_xyhbond_nbd_refined 0.097 r_symmetry_xyhbond_nbd_refined 0.094 r_gen_planes_refined 0.009 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5708 Nucleic Acid Atoms Solvent Atoms 709 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing