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Complex between S. aureus aureolysin and IMPI mutant I57I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SSB 3SSB, 1BQB experimental model PDB 1BQB 3SSB, 1BQB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Best crystals of aureolysin in complex with IMPI mutant I57F were obtained at 20 dgrees 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 2.34 47.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.08 α = 90 b = 68.08 β = 90 c = 166.69 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 1.6 68.1 99.7 0.05 0.029 0.999 14.2 4 99152 34.4
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 1.6 1.7 99.4 1.069 0.618 0.999 1.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3SSB, 1BQB 1.6 68.08 99151 681 99.706 0.158 0.1579 0.1592 0.1878 0.1849 32.642
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] 10.816 10.816 -21.633
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.058 r_dihedral_angle_3_deg 16.787 r_dihedral_angle_4_deg 12.014 r_dihedral_angle_1_deg 7.56 r_lrange_it 4.481 r_scangle_it 2.845 r_mcangle_it 2.486 r_scbond_it 2.052 r_mcbond_it 1.781 r_angle_refined_deg 1.757
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.058 r_dihedral_angle_3_deg 16.787 r_dihedral_angle_4_deg 12.014 r_dihedral_angle_1_deg 7.56 r_lrange_it 4.481 r_scangle_it 2.845 r_mcangle_it 2.486 r_scbond_it 2.052 r_mcbond_it 1.781 r_angle_refined_deg 1.757 r_nbtor_refined 0.284 r_nbd_refined 0.175 r_symmetry_nbd_refined 0.169 r_chiral_restr 0.15 r_xyhbond_nbd_refined 0.095 r_symmetry_xyhbond_nbd_refined 0.071 r_gen_planes_refined 0.01 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5715 Nucleic Acid Atoms Solvent Atoms 559 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing