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Structural insights into the elevator-like mechanism of the sodium/citrate symporter CitS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A1S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 100 mM MES pH 6.0-6.5, 100-200 mM NaCl, 32-36% PEG400
Crystal Properties Matthews coefficient Solvent content 3.79 67.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.668 α = 86.1 b = 91.874 β = 82.22 c = 96.32 γ = 69.66
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 MAR CCD 130 mm 2016-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.979 PAL/PLS 7A (6B, 6C1)
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 3.76 95.41 99.2 21.2 1.9 26874
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.8 3.9 98.6 1.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5A1S 3.76 95.41 25473 1401 94.95 0.26908 0.26748 0.29815 0.3077 RANDOM 238.985
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] -14.59 4.45 -4.59 2.51 -2.87 13.15
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 34.492 r_long_range_B_other 34.492 r_dihedral_angle_2_deg 32.026 r_mcangle_it 22.106 r_mcangle_other 22.104 r_scangle_other 20.252 r_dihedral_angle_3_deg 13.869 r_mcbond_other 13.817 r_mcbond_it 13.816 r_dihedral_angle_4_deg 13.205
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 34.492 r_long_range_B_other 34.492 r_dihedral_angle_2_deg 32.026 r_mcangle_it 22.106 r_mcangle_other 22.104 r_scangle_other 20.252 r_dihedral_angle_3_deg 13.869 r_mcbond_other 13.817 r_mcbond_it 13.816 r_dihedral_angle_4_deg 13.205 r_scbond_it 12.207 r_scbond_other 12.207 r_dihedral_angle_1_deg 4.463 r_angle_other_deg 1.609 r_angle_refined_deg 1.503 r_chiral_restr 0.156 r_bond_refined_d 0.01 r_bond_other_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.007 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 12271 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing