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Crystal structure of catalytic domain of LytB (E585Q) from Streptococcus pneumoniae in complex with NAG-NAM-NAG-NAM-NAG peptidolycan analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7PJ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 PEG 300
Bis-Tris
Calcium acetate
Crystal Properties Matthews coefficient Solvent content 2.21 44.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.291 α = 90 b = 92.543 β = 90 c = 124.795 γ = 90
Symmetry Space Group C 2 2 21
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 6M 2019-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979260 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.3 46.27 99.9 0.065 0.019 19.6 13 67551
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.32 0.765 0.222
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7PJ3 1.3 46.254 67509 3387 99.883 0.15 0.1491 0.1492 0.1745 0.1746 20.59
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] 1.142 -0.845 -0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.965 r_dihedral_angle_4_deg 22.02 r_dihedral_angle_3_deg 11.791 r_dihedral_angle_1_deg 6.365 r_rigid_bond_restr 3.492 r_scangle_it 3.224 r_scangle_other 3.223 r_lrange_it 3.207 r_lrange_other 3.151 r_scbond_other 2.721
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.965 r_dihedral_angle_4_deg 22.02 r_dihedral_angle_3_deg 11.791 r_dihedral_angle_1_deg 6.365 r_rigid_bond_restr 3.492 r_scangle_it 3.224 r_scangle_other 3.223 r_lrange_it 3.207 r_lrange_other 3.151 r_scbond_other 2.721 r_scbond_it 2.72 r_mcangle_other 1.974 r_mcangle_it 1.973 r_angle_refined_deg 1.677 r_angle_other_deg 1.626 r_mcbond_it 1.6 r_mcbond_other 1.592 r_nbd_other 0.246 r_symmetry_nbd_refined 0.233 r_nbd_refined 0.221 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.175 r_symmetry_xyhbond_nbd_refined 0.171 r_metal_ion_refined 0.163 r_symmetry_metal_ion_refined 0.149 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.094 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.01 r_bond_other_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2174 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 115
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing