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Crystal structure of the catalytic module of a family 98 glycoside hydrolase from Streptococcus pneumoniae TIGR4 (Sp4GH98) in its native form.
Crystallization Crystal Properties Matthews coefficient Solvent content 1.88 34.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.84 α = 90 b = 90.49 β = 90 c = 116.78 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 1.5 20 84.7 0.06 20.3 6.2 69668 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 1.5 38.35 69668 3678 84.26 0.12571 0.12389 0.1334 0.15982 0.1647 RANDOM 10.261
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] 0.19 -0.14 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.21 r_dihedral_angle_4_deg 19.376 r_dihedral_angle_3_deg 12.462 r_dihedral_angle_1_deg 9.086 r_sphericity_free 7.057 r_scangle_it 3.923 r_scbond_it 2.998 r_sphericity_bonded 2.538 r_mcangle_it 1.855 r_angle_refined_deg 1.597
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.21 r_dihedral_angle_4_deg 19.376 r_dihedral_angle_3_deg 12.462 r_dihedral_angle_1_deg 9.086 r_sphericity_free 7.057 r_scangle_it 3.923 r_scbond_it 2.998 r_sphericity_bonded 2.538 r_mcangle_it 1.855 r_angle_refined_deg 1.597 r_mcbond_it 1.558 r_rigid_bond_restr 1.536 r_angle_other_deg 0.995 r_mcbond_other 0.544 r_symmetry_hbond_refined 0.392 r_symmetry_vdw_other 0.252 r_nbd_refined 0.224 r_nbd_other 0.2 r_symmetry_vdw_refined 0.185 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.164 r_chiral_restr 0.108 r_nbtor_other 0.083 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.001 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 4503 Nucleic Acid Atoms Solvent Atoms 600 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement