☰ Navigation Tabs
Crystal structure of catalytic domain of LytB (E585Q) from Streptococcus pneumoniae in complex with NAG-NAM-NAG-NAM tetrasaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7PL3
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 2.2 44.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.144 α = 90 b = 92.522 β = 90 c = 124.572 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 2019-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 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 1.5 46.26 99.5 0.048 0.016 24 9.9 43792 18.52
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 1.5 1.53 0.66 0.217
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 7PL3 1.5 46.254 43749 2221 99.344 0.147 0.145 0.145 0.1938 0.1938 22.101
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] 2.451 -1.387 -1.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.736 r_dihedral_angle_4_deg 22.626 r_dihedral_angle_3_deg 12.2 r_dihedral_angle_1_deg 6.55 r_rigid_bond_restr 6.544 r_scangle_it 4.091 r_scangle_other 4.089 r_lrange_it 4.018 r_lrange_other 3.982 r_scbond_it 3.652
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.736 r_dihedral_angle_4_deg 22.626 r_dihedral_angle_3_deg 12.2 r_dihedral_angle_1_deg 6.55 r_rigid_bond_restr 6.544 r_scangle_it 4.091 r_scangle_other 4.089 r_lrange_it 4.018 r_lrange_other 3.982 r_scbond_it 3.652 r_scbond_other 3.652 r_mcangle_other 2.542 r_mcangle_it 2.541 r_mcbond_it 2.179 r_mcbond_other 2.175 r_angle_refined_deg 1.748 r_angle_other_deg 1.73 r_nbd_other 0.283 r_symmetry_metal_ion_refined 0.241 r_symmetry_nbd_refined 0.217 r_nbd_refined 0.213 r_symmetry_nbd_other 0.2 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.153 r_symmetry_xyhbond_nbd_refined 0.133 r_metal_ion_refined 0.131 r_symmetry_xyhbond_nbd_other 0.102 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.076 r_bond_other_d 0.018 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2174 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing