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Crystal Structure of Streptococcus pneumoniae NanC, in complex with 3-Sialyllactose
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 20% PEG3350, 0.25M Ammonium sulfate, 0.1M Hepes pH8, 7.5% Isopropanol
Crystal Properties Matthews coefficient Solvent content 2.48 50.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.47 α = 90 b = 136.57 β = 90 c = 150.07 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 100 PIXEL DECTRIS PILATUS 2M 2011-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9173 Diamond I04-1
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 2.27 75.04 99.7 0.326 6 4.5 70273
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.27 2.33 99.9 1.375 2.5 4.6
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 MOLECULAR REPLACEMENT THROUGHOUT 2.27 75.04 66621 3538 99.46 0.2208 0.2182 0.2242 0.2692 0.2732 RANDOM 21.429
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] -1.28 2.96 -1.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.6 r_dihedral_angle_3_deg 13.771 r_dihedral_angle_4_deg 9.879 r_dihedral_angle_1_deg 7.226 r_mcangle_it 3.097 r_mcbond_it 2.063 r_mcbond_other 2.063 r_angle_refined_deg 1.466 r_angle_other_deg 1.012 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.6 r_dihedral_angle_3_deg 13.771 r_dihedral_angle_4_deg 9.879 r_dihedral_angle_1_deg 7.226 r_mcangle_it 3.097 r_mcbond_it 2.063 r_mcbond_other 2.063 r_angle_refined_deg 1.466 r_angle_other_deg 1.012 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10378 Nucleic Acid Atoms Solvent Atoms 721 Heterogen Atoms 154
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction xia2 data scaling