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Extracellular serine protease Jep from mouse-adapted S. aureus strain JSNZ
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.8 293 0.2M potassium sulfate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.99 38.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.261 α = 90 b = 49.488 β = 113.324 c = 68.383 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 EIGER X 16M 2024-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.72932 PETRA III, EMBL c/o DESY P13 (MX1)
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 0.98 29.62 97.4 0.09 0.106 0.055 0.994 9.3 7 101075 -3 9.65
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 0.98 1 95.5 0.987 1.166 0.615 0.755 6.9
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 0.98 29.62 101074 5213 97.204 0.148 0.1476 0.1467 0.1625 0.1628 16.481
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] 0.381 0.58 -0.486 -0.288
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.425 r_lrange_it 15.45 r_dihedral_angle_6_deg 15.158 r_lrange_other 13.679 r_dihedral_angle_3_deg 11.001 r_scangle_it 7.858 r_scangle_other 7.77 r_dihedral_angle_1_deg 6.516 r_mcangle_other 5.955 r_mcangle_it 5.947
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.425 r_lrange_it 15.45 r_dihedral_angle_6_deg 15.158 r_lrange_other 13.679 r_dihedral_angle_3_deg 11.001 r_scangle_it 7.858 r_scangle_other 7.77 r_dihedral_angle_1_deg 6.516 r_mcangle_other 5.955 r_mcangle_it 5.947 r_scbond_it 5.586 r_scbond_other 5.51 r_mcbond_it 4.14 r_mcbond_other 4.129 r_rigid_bond_restr 3.799 r_angle_refined_deg 1.781 r_symmetry_xyhbond_nbd_other 0.771 r_angle_other_deg 0.655 r_symmetry_nbd_refined 0.435 r_nbd_other 0.358 r_nbd_refined 0.258 r_symmetry_nbd_other 0.199 r_symmetry_xyhbond_nbd_refined 0.195 r_xyhbond_nbd_refined 0.186 r_nbtor_refined 0.172 r_metal_ion_refined 0.126 r_chiral_restr 0.105 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.011 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 1513 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement Coot model building PHASER phasing XDS data scaling XDS data reduction MxCuBE data collection