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Crystal structure of choline-binding module (R1-R9) of LytB from Streptococcus pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V05
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 MES buffer
Zinc sulfate
PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.41 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.299 α = 90 b = 96.143 β = 100.966 c = 49.096 γ = 90
Symmetry Space Group P 1 21 1
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 2017-03-09 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 1.99 48.2 98.7 0.238 0.108 6 5.5 28181
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 1.99 2.03 0.952 0.496
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 2V05 1.99 44.504 28134 1439 99.245 0.175 0.1723 0.1814 0.2328 0.2326 25.524
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] 0.866 1.014 -0.332 -0.862
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.769 r_dihedral_angle_4_deg 34.099 r_dihedral_angle_3_deg 17.074 r_lrange_it 7.704 r_lrange_other 7.7 r_dihedral_angle_1_deg 7.298 r_scangle_it 5.998 r_scangle_other 5.996 r_mcangle_it 4.202 r_mcangle_other 4.202
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.769 r_dihedral_angle_4_deg 34.099 r_dihedral_angle_3_deg 17.074 r_lrange_it 7.704 r_lrange_other 7.7 r_dihedral_angle_1_deg 7.298 r_scangle_it 5.998 r_scangle_other 5.996 r_mcangle_it 4.202 r_mcangle_other 4.202 r_scbond_it 3.98 r_scbond_other 3.979 r_mcbond_it 2.983 r_mcbond_other 2.974 r_angle_refined_deg 1.827 r_angle_other_deg 1.512 r_nbd_other 0.293 r_nbd_refined 0.207 r_symmetry_nbd_other 0.2 r_symmetry_nbd_refined 0.196 r_nbtor_refined 0.195 r_symmetry_xyhbond_nbd_refined 0.173 r_xyhbond_nbd_refined 0.165 r_symmetry_metal_ion_refined 0.121 r_ncsr_local_group_1 0.108 r_symmetry_nbtor_other 0.09 r_chiral_restr 0.089 r_symmetry_xyhbond_nbd_other 0.072 r_metal_ion_refined 0.049 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3029 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MoRDa phasing