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Staphylococcus aureus-specific lysin L1-3 (LysM-CHAP) covalently complexed to Pep1a-CMK substrate mimic
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CSH in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 25% PEG MME 5000, 0.1 M TRIS pH 8.5, 0.2 M lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.994 α = 90 b = 135.046 β = 90 c = 57.626 γ = 90
Symmetry Space Group C 2 2 21
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 2024-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97625 PETRA III, EMBL c/o DESY P13 (MX1)
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 2.83 30.03 99.8 0.335 0.194 0.971 4.8 7.2 6204
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 2.83 2.9 1.517 1.755 0.571 1.4
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 2.83 30.01 6204 310 99.4 0.25698 0.25592 0.2658 0.27763 0.2803 RANDOM 35.236
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] -3.82 6.65 -2.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.509 r_dihedral_angle_3_deg 10.185 r_dihedral_angle_1_deg 5.348 r_long_range_B_refined 2.144 r_long_range_B_other 2.143 r_scangle_other 0.805 r_angle_refined_deg 0.711 r_mcangle_it 0.634 r_mcangle_other 0.634 r_scbond_it 0.434
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.509 r_dihedral_angle_3_deg 10.185 r_dihedral_angle_1_deg 5.348 r_long_range_B_refined 2.144 r_long_range_B_other 2.143 r_scangle_other 0.805 r_angle_refined_deg 0.711 r_mcangle_it 0.634 r_mcangle_other 0.634 r_scbond_it 0.434 r_scbond_other 0.434 r_mcbond_it 0.336 r_mcbond_other 0.336 r_angle_other_deg 0.279 r_chiral_restr 0.032 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 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 1550 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction xia2 data scaling PHASER phasing