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Structural characterization of a carbohydrate substrate binding protein from Streptococcus pneumoniae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.02 M Mes pH 6.5, 0.2 M NaCl, 2.5% glycerol and 0.5 mM TCEP
Crystal Properties Matthews coefficient Solvent content 2.27 45.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.24 α = 90 b = 82.54 β = 107.76 c = 60.35 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M KB mirrors 2016-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) CC (Half) 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 1.61 49.64 99.9 0.023 0.028 0.999 16.4 6.6 62913 20.01
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.61 1.65 99.6 0.443 0.578 4 6.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.61 49.64 59803 3158 99.94 0.19469 0.19292 0.2055 0.22871 0.2382 RANDOM 25.227
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 39.326 r_dihedral_angle_4_deg 18.735 r_dihedral_angle_3_deg 12.85 r_long_range_B_refined 6.192 r_long_range_B_other 6.013 r_dihedral_angle_1_deg 5.87 r_scangle_other 3.404 r_mcangle_it 2.72 r_mcangle_other 2.719 r_scbond_it 2.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.326 r_dihedral_angle_4_deg 18.735 r_dihedral_angle_3_deg 12.85 r_long_range_B_refined 6.192 r_long_range_B_other 6.013 r_dihedral_angle_1_deg 5.87 r_scangle_other 3.404 r_mcangle_it 2.72 r_mcangle_other 2.719 r_scbond_it 2.081 r_scbond_other 2.081 r_mcbond_it 1.661 r_mcbond_other 1.659 r_angle_refined_deg 1.389 r_angle_other_deg 0.93 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3583 Nucleic Acid Atoms Solvent Atoms 338 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling SHELXCD phasing