☰ Navigation Tabs
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 3.44 68.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.367 α = 90 b = 163.994 β = 93.5 c = 93.67 γ = 90
Symmetry Space Group P 1 21 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 CCD MAR CCD 130 mm 2016-07-19 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 3.6 93.49 99.6 22.7 3.7 30477
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 3.6 3.7 100 1.3 3.7
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 3.62 93.49 29044 1433 98.48 0.23614 0.23459 0.26734 0.2646 RANDOM 189.555
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] 10.85 9.36 -11.48 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.39 r_long_range_B_refined 21.608 r_long_range_B_other 21.607 r_dihedral_angle_4_deg 15.859 r_dihedral_angle_3_deg 15.201 r_scangle_other 14.299 r_mcangle_it 13.782 r_mcangle_other 13.781 r_scbond_it 8.878 r_scbond_other 8.877
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.39 r_long_range_B_refined 21.608 r_long_range_B_other 21.607 r_dihedral_angle_4_deg 15.859 r_dihedral_angle_3_deg 15.201 r_scangle_other 14.299 r_mcangle_it 13.782 r_mcangle_other 13.781 r_scbond_it 8.878 r_scbond_other 8.877 r_mcbond_it 8.791 r_mcbond_other 8.788 r_dihedral_angle_1_deg 4.656 r_angle_refined_deg 1.747 r_angle_other_deg 1.336 r_chiral_restr 0.106 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.008 r_gen_planes_other 0.006 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 12355 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing