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Crystal structure of the catalytic module of a family 98 glycoside hydrolase from Streptococcus pneumoniae SP3-BS71 (Sp3GH98) in complex with the A-LewisY pentasaccharide blood group antigen.
Crystallization Crystal Properties Matthews coefficient Solvent content 2.34 46.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.9 α = 90 b = 153.7 β = 90 c = 90.88 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 292 CCD ADSC QUANTUM 315r M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 40 99.1 0.11 14.5 6.7 102091 2
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION OTHER THROUGHOUT NONE 1.9 29.12 102091 5371 99.03 0.16481 0.16248 0.1625 0.2096 0.2078 RANDOM 12.809
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.859 r_dihedral_angle_4_deg 21.562 r_dihedral_angle_3_deg 14.199 r_dihedral_angle_1_deg 6.934 r_scangle_it 4.01 r_scbond_it 2.694 r_angle_refined_deg 1.666 r_mcangle_it 1.645 r_mcbond_it 1.117 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.859 r_dihedral_angle_4_deg 21.562 r_dihedral_angle_3_deg 14.199 r_dihedral_angle_1_deg 6.934 r_scangle_it 4.01 r_scbond_it 2.694 r_angle_refined_deg 1.666 r_mcangle_it 1.645 r_mcbond_it 1.117 r_nbtor_refined 0.313 r_nbd_refined 0.212 r_symmetry_hbond_refined 0.196 r_xyhbond_nbd_refined 0.164 r_symmetry_vdw_refined 0.159 r_chiral_restr 0.132 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9359 Nucleic Acid Atoms Solvent Atoms 974 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement