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Crystal structure of Lys2972, a phage endolysin targeting Streptococcus thermophilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model RoseTTAFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5 295 0.2 M lithium chloride, 0.1 M sodium acetate pH 5.0, 20% PEG-6000
Crystal Properties Matthews coefficient Solvent content 1.98 37.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.18 α = 90 b = 64.792 β = 122.68 c = 55.426 γ = 90
Symmetry Space Group C 1 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 PILATUS3 S 6M 2022-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.27 47.6 97.6 0.043 0.999 13.6 3.3 63597
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.27 1.34 98.4 0.671 0.684 2.3 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.27 28.5 60507 3086 97.48 0.16968 0.16862 0.19083 0.2071 RANDOM 19.227
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] 0.08 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.76 r_dihedral_angle_4_deg 21.199 r_dihedral_angle_3_deg 13.899 r_dihedral_angle_1_deg 6.955 r_long_range_B_refined 5.031 r_long_range_B_other 4.929 r_scangle_other 4.045 r_scbond_it 2.696 r_scbond_other 2.694 r_mcangle_it 2.444
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.76 r_dihedral_angle_4_deg 21.199 r_dihedral_angle_3_deg 13.899 r_dihedral_angle_1_deg 6.955 r_long_range_B_refined 5.031 r_long_range_B_other 4.929 r_scangle_other 4.045 r_scbond_it 2.696 r_scbond_other 2.694 r_mcangle_it 2.444 r_mcangle_other 2.443 r_angle_refined_deg 1.938 r_mcbond_it 1.702 r_mcbond_other 1.701 r_angle_other_deg 1.599 r_chiral_restr 0.117 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_bond_other_d 0.001 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 2130 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement SCALA data scaling XDS data reduction PHASER phasing