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Cell wall binding domain of the Staphylococcal phage 2638A endolysin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LEO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 292 Protein buffer: 20 mM Tris, 150 mM NaCl, pH 7.4
Crystallization buffer: 1% (W/V) tryptone, 0.05 M HEPES, pH 7.0, 12% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.64 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.13 α = 111.01 b = 62.51 β = 108.387 c = 66.171 γ = 90.184
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 2019-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.488 44.11 90.91 0.087 0.117 0.077 0.992 4.31 2.06 51577 51.65
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.488 2.57 79.34 0.678 0.907 0.598 0.486 0.68
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5LEO 2.49 44.11 1.22 27918 2586 84.04 0.2517 0.2498 0.2509 0.2859 0.2853 51.73
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 9.8921 f_angle_d 0.4692 f_chiral_restr 0.0449 f_plane_restr 0.0024 f_bond_d 0.0021
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6088 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 30
Software Software Software Name Purpose XDS data reduction XDS data scaling MOLREP phasing PHENIX refinement Coot model building