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Crystal structure of catalytic domain in open conformation of LytB from Streptococcus pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Q2W
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 44.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.276 α = 90 b = 92.614 β = 90 c = 124.392 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 0.97926 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 1.43 46.31 100 0.04 0.012 31 13.1 50892
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 1.43 1.45 0.775 0.219
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 4Q2W 1.43 43.434 50848 2535 99.994 0.146 0.1438 0.1438 0.1852 0.1855 22.694
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] 2.288 -1.56 -0.729
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.545 r_dihedral_angle_4_deg 17.141 r_dihedral_angle_3_deg 11.689 r_dihedral_angle_1_deg 6.498 r_rigid_bond_restr 6.45 r_scangle_it 4.027 r_scangle_other 4.026 r_lrange_it 3.987 r_lrange_other 3.897 r_scbond_it 3.421
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.545 r_dihedral_angle_4_deg 17.141 r_dihedral_angle_3_deg 11.689 r_dihedral_angle_1_deg 6.498 r_rigid_bond_restr 6.45 r_scangle_it 4.027 r_scangle_other 4.026 r_lrange_it 3.987 r_lrange_other 3.897 r_scbond_it 3.421 r_scbond_other 3.42 r_mcangle_other 2.496 r_mcangle_it 2.492 r_mcbond_it 2.163 r_mcbond_other 2.073 r_angle_other_deg 1.727 r_angle_refined_deg 1.597 r_nbd_other 0.256 r_symmetry_xyhbond_nbd_refined 0.255 r_nbd_refined 0.215 r_symmetry_nbd_other 0.204 r_metal_ion_refined 0.203 r_symmetry_nbd_refined 0.196 r_symmetry_metal_ion_refined 0.193 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.154 r_symmetry_xyhbond_nbd_other 0.124 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.079 r_bond_other_d 0.018 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2174 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing