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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 B-trisaccharide blood group antigen.
Crystallization Crystal Properties Matthews coefficient Solvent content 2.37 47.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.07 α = 90 b = 154.18 β = 90 c = 91.15 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 2 40 84.6 0.06 21.9 6.1 74917 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 2 39.94 74917 3942 84 0.16331 0.16079 0.1606 0.21085 0.2077 RANDOM 13.139
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 37.231 r_dihedral_angle_4_deg 21.268 r_dihedral_angle_3_deg 14.783 r_dihedral_angle_1_deg 7.843 r_scangle_it 3.187 r_scbond_it 2.129 r_angle_refined_deg 1.474 r_mcangle_it 1.329 r_mcbond_it 0.857 r_symmetry_hbond_refined 0.329
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.231 r_dihedral_angle_4_deg 21.268 r_dihedral_angle_3_deg 14.783 r_dihedral_angle_1_deg 7.843 r_scangle_it 3.187 r_scbond_it 2.129 r_angle_refined_deg 1.474 r_mcangle_it 1.329 r_mcbond_it 0.857 r_symmetry_hbond_refined 0.329 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.208 r_nbd_refined 0.204 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.114 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 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 9354 Nucleic Acid Atoms Solvent Atoms 980 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement