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Endolysin from Escherichia coli O157:H7 phage FAHEc1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ET6 6ET6A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.1 M Sodium Chloride, 1.6 M Ammonium sulfate, 0.1 M Sodium HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.28 46.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.874 α = 90 b = 67.874 β = 90 c = 134.437 γ = 120
Symmetry Space Group P 32 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 110 PIXEL DECTRIS EIGER X 16M 2019-08-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.954 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.71 44.85 99.9 0.999 13.7 1 39675
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.71 1.74 98 0.575 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6ET6A 1.71 44.85 37676 2004 99.85 0.17503 0.17347 0.1843 0.203 0.2074 RANDOM 33.766
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] -0.26 -0.13 -0.26 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.555 r_dihedral_angle_3_deg 13.709 r_dihedral_angle_4_deg 12.803 r_long_range_B_refined 6.126 r_long_range_B_other 5.985 r_dihedral_angle_1_deg 5.79 r_scangle_other 4.532 r_scbond_it 3.032 r_scbond_other 2.904 r_mcangle_other 2.652
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.555 r_dihedral_angle_3_deg 13.709 r_dihedral_angle_4_deg 12.803 r_long_range_B_refined 6.126 r_long_range_B_other 5.985 r_dihedral_angle_1_deg 5.79 r_scangle_other 4.532 r_scbond_it 3.032 r_scbond_other 2.904 r_mcangle_other 2.652 r_mcangle_it 2.65 r_mcbond_it 1.813 r_mcbond_other 1.785 r_angle_refined_deg 1.731 r_angle_other_deg 1.466 r_chiral_restr 0.091 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 2475 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing Coot model building