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Crystal structure of the CTP1L endolysin reveals how its activity is regulated by a secondary translation product
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JFX PDB ENTRIES 1JFX AND 2NW0 HYBRID MODEL experimental model PDB 2NW0 PDB ENTRIES 1JFX AND 2NW0 HYBRID MODEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5-10 % PEG 8000, 20 MM TRIS PH 8.0
Crystal Properties Matthews coefficient Solvent content 3.12 60.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.197 α = 90 b = 136.197 β = 90 c = 56.457 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC CCD KB MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 30 100 0.15 9.6 8.2 40146
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 100 0.75 2.6 8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRIES 1JFX AND 2NW0 HYBRID MODEL 1.9 19.9 40146 2132 99.87 0.16412 0.16196 0.20468 0.2207 RANDOM 26.486
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] -0.05 -0.05 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.175 r_dihedral_angle_4_deg 22.649 r_dihedral_angle_3_deg 12.808 r_dihedral_angle_1_deg 6.151 r_angle_refined_deg 1.8 r_angle_other_deg 0.865 r_chiral_restr 0.127 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.175 r_dihedral_angle_4_deg 22.649 r_dihedral_angle_3_deg 12.808 r_dihedral_angle_1_deg 6.151 r_angle_refined_deg 1.8 r_angle_other_deg 0.865 r_chiral_restr 0.127 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2780 Nucleic Acid Atoms Solvent Atoms 480 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing