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Crystal structure of catalytic domain of LytB from Streptococcus pneumoniae in complex with NAG-NAG-NAG-NAG tetrasaccharide
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 44.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.679 α = 90 b = 92.358 β = 90 c = 124.3 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 0.979260 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 1.55 46.18 100 0.058 0.017 24.5 12.8 40276
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 1.55 1.58 0.701 0.199
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 1.55 46.174 40235 1991 99.975 0.146 0.1436 0.1576 0.1917 0.2002 23.592
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] 1.171 -1.672 0.501
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.094 r_dihedral_angle_4_deg 23.472 r_dihedral_angle_3_deg 12.753 r_dihedral_angle_1_deg 6.598 r_rigid_bond_restr 5.724 r_scangle_it 4.184 r_scangle_other 4.183 r_lrange_it 4.17 r_lrange_other 4.102 r_scbond_it 3.661
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.094 r_dihedral_angle_4_deg 23.472 r_dihedral_angle_3_deg 12.753 r_dihedral_angle_1_deg 6.598 r_rigid_bond_restr 5.724 r_scangle_it 4.184 r_scangle_other 4.183 r_lrange_it 4.17 r_lrange_other 4.102 r_scbond_it 3.661 r_scbond_other 3.66 r_mcangle_other 3.103 r_mcangle_it 3.1 r_mcbond_it 2.769 r_mcbond_other 2.741 r_angle_other_deg 1.931 r_angle_refined_deg 1.668 r_nbd_other 0.323 r_symmetry_nbd_refined 0.258 r_symmetry_metal_ion_refined 0.229 r_symmetry_xyhbond_nbd_refined 0.212 r_nbd_refined 0.208 r_symmetry_nbd_other 0.206 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.152 r_metal_ion_refined 0.119 r_symmetry_xyhbond_nbd_other 0.111 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.082 r_bond_other_d 0.018 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2174 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing