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Crystal structure of the catalytic module of a family 98 glycoside hydrolase from Streptococcus pneumoniae TIGR4 in complex with the H- disaccharide blood group antigen.
Crystallization Crystal Properties Matthews coefficient Solvent content 1.86 33.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.796 α = 90 b = 90.816 β = 90 c = 116.545 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS NSLS X8C
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 1.7 20 97.4 0.13 16.9 3.9 55648 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 1.7 19.43 55648 2961 97.27 0.14603 0.14337 0.1535 0.19709 0.205 RANDOM 8.571
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] -0.02 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.311 r_dihedral_angle_4_deg 21.247 r_dihedral_angle_3_deg 12.865 r_dihedral_angle_1_deg 6.528 r_sphericity_free 6.483 r_scangle_it 3.549 r_scbond_it 2.662 r_sphericity_bonded 2.323 r_mcangle_it 1.634 r_angle_refined_deg 1.524
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.311 r_dihedral_angle_4_deg 21.247 r_dihedral_angle_3_deg 12.865 r_dihedral_angle_1_deg 6.528 r_sphericity_free 6.483 r_scangle_it 3.549 r_scbond_it 2.662 r_sphericity_bonded 2.323 r_mcangle_it 1.634 r_angle_refined_deg 1.524 r_rigid_bond_restr 1.357 r_mcbond_it 1.331 r_angle_other_deg 0.974 r_mcbond_other 0.441 r_symmetry_hbond_refined 0.255 r_symmetry_vdw_other 0.247 r_nbd_refined 0.214 r_nbd_other 0.201 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.174 r_symmetry_vdw_refined 0.15 r_chiral_restr 0.099 r_nbtor_other 0.086 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4490 Nucleic Acid Atoms Solvent Atoms 642 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement