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CHAP domain of Staphylococcus aureus-specific lysin L1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CSH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20 mM HEPES 7.4, 2 mM TCEP, 150 mM sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.63 53.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.12 α = 86.07 b = 57.43 β = 85.22 c = 63.05 γ = 83.99
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 9M 2023-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.95372 CLSI 08ID-1
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 1.25 36.64 94.5 0.042 0.042 0.998 14.8 3.6 165929
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 1.25 1.28 0.234 0.234 0.937 5
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 1.25 36.64 165929 8683 94.49 0.18783 0.18726 0.1963 0.19894 0.2086 RANDOM 10.086
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] 0.46 0.4 -0.06 -0.22 -0.03 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.162 r_dihedral_angle_1_deg 6.92 r_dihedral_angle_2_deg 3.109 r_long_range_B_refined 2.396 r_long_range_B_other 2.396 r_angle_refined_deg 1.021 r_mcangle_it 0.673 r_mcangle_other 0.673 r_scangle_other 0.537 r_angle_other_deg 0.381
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.162 r_dihedral_angle_1_deg 6.92 r_dihedral_angle_2_deg 3.109 r_long_range_B_refined 2.396 r_long_range_B_other 2.396 r_angle_refined_deg 1.021 r_mcangle_it 0.673 r_mcangle_other 0.673 r_scangle_other 0.537 r_angle_other_deg 0.381 r_mcbond_it 0.362 r_mcbond_other 0.362 r_scbond_it 0.293 r_scbond_other 0.293 r_chiral_restr 0.054 r_gen_planes_refined 0.003 r_bond_refined_d 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 4522 Nucleic Acid Atoms Solvent Atoms 600 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction xia2 data scaling PHASER phasing