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Extracellular serine protease Jep from mouse-adapted S. aureus strain JSNZ in complex with inhibitor AEBSF
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9S74
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.15M ammonium iodide, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.16 43.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 272.143 α = 90 b = 49.508 β = 96.043 c = 67.304 γ = 90
Symmetry Space Group C 1 2 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 PILATUS3 6M 2025-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 1.8 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.8 45.26 93.9 0.077 0.093 0.051 0.997 10.1 5.6 78159 -3 16.44
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 50.4 0.307 0.416 0.279 0.627 2.5 3.1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.8 45.26 78158 3876 93.916 0.222 0.2195 0.2178 0.2616 0.261 28.753
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] 1.154 0.285 -1.963 0.732
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.262 r_dihedral_angle_3_deg 14.133 r_dihedral_angle_2_deg 8.762 r_lrange_it 7.272 r_lrange_other 7.226 r_dihedral_angle_1_deg 6.918 r_rigid_bond_restr 4.265 r_scangle_it 4.179 r_scangle_other 4.178 r_mcangle_it 3.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.262 r_dihedral_angle_3_deg 14.133 r_dihedral_angle_2_deg 8.762 r_lrange_it 7.272 r_lrange_other 7.226 r_dihedral_angle_1_deg 6.918 r_rigid_bond_restr 4.265 r_scangle_it 4.179 r_scangle_other 4.178 r_mcangle_it 3.5 r_mcangle_other 3.5 r_scbond_it 2.754 r_scbond_other 2.753 r_mcbond_it 2.223 r_mcbond_other 2.222 r_angle_refined_deg 1.928 r_angle_other_deg 0.655 r_symmetry_xyhbond_nbd_refined 0.454 r_xyhbond_nbd_other 0.397 r_symmetry_nbd_refined 0.327 r_nbd_other 0.282 r_nbd_refined 0.201 r_xyhbond_nbd_refined 0.197 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.173 r_metal_ion_refined 0.126 r_symmetry_xyhbond_nbd_other 0.112 r_chiral_restr 0.096 r_symmetry_nbtor_other 0.088 r_ncsr_local_group_3 0.066 r_ncsr_local_group_8 0.066 r_ncsr_local_group_6 0.062 r_ncsr_local_group_7 0.062 r_ncsr_local_group_1 0.06 r_ncsr_local_group_10 0.06 r_ncsr_local_group_9 0.059 r_ncsr_local_group_4 0.058 r_ncsr_local_group_2 0.056 r_ncsr_local_group_5 0.045 r_ext_dist_refined_b 0.019 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7745 Nucleic Acid Atoms Solvent Atoms 439 Heterogen Atoms 123
Software Software Software Name Purpose REFMAC refinement Coot model building PHASER phasing XDS data scaling XDS data reduction MxCuBE data collection