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Substrate-bound outward-open state of a Na+-coupled sialic acid symporter reveals a novel Na+-site
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1M sodium citrate pH 5, 0.2-0.5M potassium chloride, 30-40% pentaerythritol propoxylate (5/4/PO/OH)
Crystal Properties Matthews coefficient Solvent content 3.19 61.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.59 α = 90 b = 98.07 β = 92.15 c = 54.78 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 PILATUS3 S 6M 2015-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.97858 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.95 78.4 99.2 6.43 3.24 49833
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 THROUGHOUT 1.95 78.4 47316 2536 99.22 0.20104 0.19882 0.2136 0.24346 0.2557 RANDOM 29.973
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] 2.91 0.17 -1.27 -1.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.932 r_dihedral_angle_4_deg 15.148 r_dihedral_angle_3_deg 14.169 r_long_range_B_refined 6.322 r_long_range_B_other 6.131 r_dihedral_angle_1_deg 5.626 r_scangle_other 4.268 r_scbond_it 2.995 r_scbond_other 2.954 r_mcangle_other 2.935
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.932 r_dihedral_angle_4_deg 15.148 r_dihedral_angle_3_deg 14.169 r_long_range_B_refined 6.322 r_long_range_B_other 6.131 r_dihedral_angle_1_deg 5.626 r_scangle_other 4.268 r_scbond_it 2.995 r_scbond_other 2.954 r_mcangle_other 2.935 r_mcangle_it 2.934 r_mcbond_it 2.111 r_mcbond_other 2.107 r_angle_refined_deg 1.735 r_angle_other_deg 0.925 r_chiral_restr 0.108 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_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 3707 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling SHELXS phasing