☰ Navigation Tabs
Crystal structure of active form of P1 phage endolysin Lyz
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.5 291.15 PEG400, Sodium citrate, pH 4.5, VAPOR DIFFUSION, temperature 291.15K
Crystal Properties Matthews coefficient Solvent content 2.51 50.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.871 α = 90 b = 66.871 β = 90 c = 166.796 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 CCD CUSTOM-MADE M MAD 2 1 x-ray CCD ADSC QUANTUM 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.979316, 0.97945, 0.953 APS 19-ID 2 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 1,2 1.75 50 96.1 0.064 17.4 22274
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) 1.75 1.81 91 0.406 10.5 2053
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 MAD THROUGHOUT 1.75 50 22274 22274 1149 96.44 0.209 0.209 0.208 0.238 RANDOM 38.337
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] -1.41 -0.71 -1.41 2.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.233 r_dihedral_angle_4_deg 18.051 r_dihedral_angle_3_deg 16.006 r_dihedral_angle_1_deg 5.789 r_scangle_it 2.694 r_scbond_it 1.941 r_angle_refined_deg 1.485 r_mcangle_it 1.013 r_angle_other_deg 0.797 r_mcbond_it 0.787
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.233 r_dihedral_angle_4_deg 18.051 r_dihedral_angle_3_deg 16.006 r_dihedral_angle_1_deg 5.789 r_scangle_it 2.694 r_scbond_it 1.941 r_angle_refined_deg 1.485 r_mcangle_it 1.013 r_angle_other_deg 0.797 r_mcbond_it 0.787 r_symmetry_hbond_refined 0.303 r_symmetry_vdw_other 0.272 r_nbd_refined 0.241 r_nbd_other 0.218 r_xyhbond_nbd_refined 0.188 r_symmetry_hbond_other 0.179 r_mcbond_other 0.179 r_symmetry_vdw_refined 0.121 r_chiral_restr 0.101 r_nbtor_other 0.091 r_xyhbond_nbd_other 0.056 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1365 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 26
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction Adxv data processing SHARP phasing