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Crystal structure of N-glycan transport solute binding protein (NgtS) from Streptococcus pneumoniae in complex with Man1GlcNAc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5SUO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 23 % PEG 3350, 0.18 M sodium bromide, 0.1 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.16 43.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.99 α = 89.17 b = 50.47 β = 89.02 c = 107.89 γ = 88.9
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 325 mm CCD 2013-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 1.04007 SSRL BL9-2
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 3 107.86 97 0.137 6.6 2.2 16399
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 MOLECULAR REPLACEMENT THROUGHOUT 5SUO 3 107.86 15579 820 97.02 0.2294 0.2268 0.2267 0.2809 0.2808 RANDOM 38.186
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] -1.17 -0.34 1.3 -2.78 0.31 3.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.183 r_dihedral_angle_4_deg 16.185 r_dihedral_angle_3_deg 14.617 r_dihedral_angle_1_deg 4.343 r_mcangle_it 1.282 r_angle_refined_deg 0.835 r_mcbond_it 0.714 r_scbond_it 0.587 r_chiral_restr 0.056 r_bond_refined_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.183 r_dihedral_angle_4_deg 16.185 r_dihedral_angle_3_deg 14.617 r_dihedral_angle_1_deg 4.343 r_mcangle_it 1.282 r_angle_refined_deg 0.835 r_mcbond_it 0.714 r_scbond_it 0.587 r_chiral_restr 0.056 r_bond_refined_d 0.004 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6878 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 54
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Aimless data scaling