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CHAP domain of Staphylococcus aureus-specific lysin L2
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 18% PEG 3350, 0.2 M potassium thiocyanate
Crystal Properties Matthews coefficient Solvent content 2.39 48.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.99 α = 90 b = 71.66 β = 90 c = 85.46 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 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 1.15 33.04 99.6 0.04 0.025 0.998 19.9 6.9 52726
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 1.15 1.18 0.496 0.403 0.791 2.2
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 1.15 33.04 52726 2860 99.53 0.21474 0.21409 0.2225 0.22664 0.2358 RANDOM 14.816
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.192 r_dihedral_angle_1_deg 6.784 r_dihedral_angle_2_deg 3.523 r_long_range_B_refined 2.513 r_long_range_B_other 2.365 r_angle_refined_deg 0.949 r_mcangle_it 0.836 r_mcangle_other 0.835 r_scangle_other 0.798 r_mcbond_it 0.475
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.192 r_dihedral_angle_1_deg 6.784 r_dihedral_angle_2_deg 3.523 r_long_range_B_refined 2.513 r_long_range_B_other 2.365 r_angle_refined_deg 0.949 r_mcangle_it 0.836 r_mcangle_other 0.835 r_scangle_other 0.798 r_mcbond_it 0.475 r_mcbond_other 0.464 r_scbond_it 0.461 r_scbond_other 0.459 r_angle_other_deg 0.377 r_chiral_restr 0.053 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 1098 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction xia2 data scaling PHASER phasing