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Crystal structure of the catalytic module of a family 98 glycoside hydrolase from Streptococcus pneumoniae TIGR4 (Sp4GH98) in complex with the LewisY pentasaccharide blood group antigen.
Crystallization Crystal Properties Matthews coefficient Solvent content 1.97 36.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.86 α = 90 b = 90.87 β = 90 c = 116.23 γ = 90
Symmetry Space Group P 21 21 21
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 2.28 40 97.7 0.14 11 4.8 22735 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 2.3 30.29 22735 1226 97.07 0.15998 0.1564 0.1561 0.22745 0.226 RANDOM 12.945
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.49 r_dihedral_angle_4_deg 18.083 r_dihedral_angle_3_deg 14.197 r_dihedral_angle_1_deg 6.501 r_scangle_it 2.112 r_scbond_it 1.358 r_angle_refined_deg 1.304 r_mcangle_it 0.863 r_mcbond_it 0.515 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.49 r_dihedral_angle_4_deg 18.083 r_dihedral_angle_3_deg 14.197 r_dihedral_angle_1_deg 6.501 r_scangle_it 2.112 r_scbond_it 1.358 r_angle_refined_deg 1.304 r_mcangle_it 0.863 r_mcbond_it 0.515 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.296 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.178 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.09 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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 4498 Nucleic Acid Atoms Solvent Atoms 334 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement