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Crystal structure of the receptor binding protein (gp15) of Listeria phage PSA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 292 0.1 M Na Acetate, pH 4.6, 30% (v/v) PEG 400, and 0.1 M Cadmium Chloride
Crystal Properties Matthews coefficient Solvent content 3.9 68.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.7 α = 90 b = 134.7 β = 90 c = 79.36 γ = 120
Symmetry Space Group P 31 2 1
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 2018-01-30 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 1.7 44.09 99.95 0.07093 0.07473 0.02333 0.999 17.76 10.2 91053 31.86
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 1.7 1.761 99.98 2.323 2.447 0.7629 0.386 1.01
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 1.7 44.09 1.92 177095 8862 99.94 0.1917 0.1907 0.1927 0.2108 0.2138 4555 43.27
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 12.7612 f_angle_d 1.231 f_chiral_restr 0.0776 f_bond_d 0.0165 f_plane_restr 0.0086
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3758 Nucleic Acid Atoms Solvent Atoms 493 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data scaling SHELXDE phasing Coot model building