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Endolysin from Escherichia coli O157:H7 phage FTEbC1, LysT84
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NM7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 Morpheus I condition F3: 0.12 M monosaccharides [0.2 M D-glucose; 0.2 M D-mannose; 0.2 M D-galactose; 0.2 M L-fucose; 0.2 M D-xylose; 0.2 M N-acetyl-D-glucosamine] 0.1 M buffer System 1 [1.0 M imidazole; MES monohydrate (acid) pH 6.5], 30% v/v Precipitant Mix 3 [40% v/v glycerol; 20% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 5.32 76.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.928 α = 90 b = 106.928 β = 90 c = 369.259 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 PIXEL DECTRIS EIGER X 16M 2019-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
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 2.99 49.04 99.9 0.521 0.535 0.124 0.974 6.6 18.5 26401
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 2.99 3.17 99.5 3.403 3.509 0.841 0.554 17.1
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 5NM7 2.99 49.04 1.92 26300 1333 99.91 0.2346 0.2326 0.2333 0.2722 0.2733 62.27
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 4.8405 f_angle_d 0.5187 f_chiral_restr 0.0362 f_plane_restr 0.0036 f_bond_d 0.0024
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3982 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 24
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing