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X-ray structure of LysECD7 endolysin against Gram-negative bacteria
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other ARCIMBOLDO light
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 0.2 M Ammonium sulfate, 20% w/v Polyethylene glycol 3,350 pH 6.0
Crystal Properties Matthews coefficient Solvent content 3.54 65.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.568 α = 90 b = 82.334 β = 90 c = 64.604 γ = 90
Symmetry Space Group C 2 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 100 PIXEL DECTRIS PILATUS 2M 2020-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.49 42.174 97.4 0.99 13.04 6 10864
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.49 2.56 93.83 0.81
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.49 42.174 7026 691 95.657 0.276 0.2675 0.2688 0.358 0.3606 58.967
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] 0.324 -0.36 0.036
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 25.294 r_dihedral_angle_2_deg 24.991 r_dihedral_angle_3_deg 18.957 r_lrange_it 10.418 r_dihedral_angle_1_deg 7.56 r_scangle_it 6.229 r_mcangle_it 6.023 r_scbond_it 4.045 r_mcbond_it 3.873 r_angle_refined_deg 1.175
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 25.294 r_dihedral_angle_2_deg 24.991 r_dihedral_angle_3_deg 18.957 r_lrange_it 10.418 r_dihedral_angle_1_deg 7.56 r_scangle_it 6.229 r_mcangle_it 6.023 r_scbond_it 4.045 r_mcbond_it 3.873 r_angle_refined_deg 1.175 r_symmetry_nbd_refined 0.392 r_nbtor_refined 0.312 r_symmetry_xyhbond_nbd_refined 0.303 r_nbd_refined 0.244 r_xyhbond_nbd_refined 0.201 r_chiral_restr 0.102 r_gen_planes_refined 0.006 r_bond_refined_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1005 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling Arcimboldo phasing