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Cell wall binding domain of endolysin from Listeria phage A500.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XOV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 292 100 mM HEPES buffer, pH 7.5, 3.3 M Sodium Chloride, 1% (v/v) glycerol.
Mixed 1:1 with protein solution (6.6-10 mg/ml; 20mM Tris, 150mM NaCl, pH 7.4)
Crystal Properties Matthews coefficient Solvent content 2.32 47.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.579 α = 90 b = 49.579 β = 90 c = 63.766 γ = 120
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 PILATUS3 S 6M 2016-01-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 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 1.587 63.7 99.1 0.159 0.168 0.055 0.993 8.5 8.99 23591 18.85
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 1.587 1.67 99.4 1.005 1.073 0.366 0.349 2.4 8.28
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 1XOV 1.59 42.94 0.37 23591 1197 98.92 0.1746 0.1485 0.1441 0.2035 0.1961 23.91
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 11.8515 f_angle_d 0.3922 f_chiral_restr 0.041 f_plane_restr 0.0031 f_bond_d 0.0013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1183 Nucleic Acid Atoms Solvent Atoms 564 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement SCALA data scaling MOSFLM data reduction PHASER phasing