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Crystal structure of a wild type endolysin LysIME-EF1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 20% PEG 3350 0.1M Tris ,pH 8.5 0.2 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.52 51.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.03 α = 90 b = 56.92 β = 96.29 c = 91.52 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 100 CCD ADSC QUANTUM 315r 2018-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97981 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.75 90.97 98 0.16 0.173 0.992 2 6.7 47634
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.8 98.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 1.75 90.97 45621 2000 97.83 0.18198 0.18017 0.1871 0.22349 0.2299 RANDOM 29.578
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.807 r_dihedral_angle_4_deg 23.132 r_dihedral_angle_3_deg 14.052 r_long_range_B_refined 7.693 r_long_range_B_other 7.529 r_dihedral_angle_1_deg 6.354 r_scangle_other 5.598 r_mcangle_it 3.767 r_mcangle_other 3.766 r_scbond_it 3.665
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.807 r_dihedral_angle_4_deg 23.132 r_dihedral_angle_3_deg 14.052 r_long_range_B_refined 7.693 r_long_range_B_other 7.529 r_dihedral_angle_1_deg 6.354 r_scangle_other 5.598 r_mcangle_it 3.767 r_mcangle_other 3.766 r_scbond_it 3.665 r_scbond_other 3.664 r_mcbond_it 2.573 r_mcbond_other 2.572 r_angle_refined_deg 1.779 r_angle_other_deg 1.024 r_chiral_restr 0.115 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 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 3389 Nucleic Acid Atoms Solvent Atoms 393 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing