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Crystal structure of secreted inactive form of P1 phage endolysin Lyz
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.5 291.15 sodium acetate, PEG4000, pH 4.5, VAPOR DIFFUSION, temperature 291.15K
Crystal Properties Matthews coefficient Solvent content 2.01 38.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.349 α = 90 b = 59.786 β = 102.51 c = 76.228 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9 APS 14-BM-C
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 1.07 50 90.2 0.057 5.6 116001
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 1.07 1.11 51.9 0.318 2.4
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.07 46.62 115921 5779 90.18 0.134 0.134 0.133 0.153 RANDOM 9.67
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] 0.23 -0.02 -0.09 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.57 r_dihedral_angle_4_deg 15.011 r_dihedral_angle_3_deg 12.281 r_sphericity_free 8.237 r_dihedral_angle_1_deg 5.335 r_scangle_it 3.935 r_scbond_it 3.334 r_sphericity_bonded 2.899 r_rigid_bond_restr 2.779 r_mcangle_it 2.378
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.57 r_dihedral_angle_4_deg 15.011 r_dihedral_angle_3_deg 12.281 r_sphericity_free 8.237 r_dihedral_angle_1_deg 5.335 r_scangle_it 3.935 r_scbond_it 3.334 r_sphericity_bonded 2.899 r_rigid_bond_restr 2.779 r_mcangle_it 2.378 r_mcbond_it 2.158 r_angle_refined_deg 1.917 r_mcbond_other 1.27 r_angle_other_deg 0.855 r_symmetry_vdw_other 0.331 r_chiral_restr 0.283 r_nbd_refined 0.239 r_nbd_other 0.209 r_xyhbond_nbd_refined 0.208 r_symmetry_hbond_refined 0.204 r_symmetry_vdw_refined 0.201 r_nbtor_other 0.093 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2430 Nucleic Acid Atoms Solvent Atoms 570 Heterogen Atoms 40
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction Adxv data processing EPMR phasing