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Crystal structure of human cystine transporter cystinosin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3P0G 3P0G, 4x5n experimental model PDB 4X5N 3P0G, 4x5n
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 6.5 293.15 12% PEG400, 80mM Li2SO4, and 50mM MES pH6.0
Crystal Properties Matthews coefficient Solvent content 3.42 64.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.51 α = 90 b = 71.27 β = 90 c = 194.64 γ = 90
Symmetry Space Group P 2 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 EIGER X 16M 2018-08-19 M SINGLE WAVELENGTH 2 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2018-07-21 M SINGLE WAVELENGTH 3 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2021-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.9794 APS 23-ID-B 2 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9794 APS 24-ID-E 3 SYNCHROTRON APS BEAMLINE 23-ID-B 0.9794 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 3.4 40.19 97.3 0.967 15.2 14.9 9815 105.72
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.4 3.52 88.9 0.722 1.69 8.3
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3P0G, 4x5n 3.4 40.19 9779 975 97.35 0.2721 0.2704 0.271 0.302 0.3039 100.5
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.9278 f_angle_d 0.7235 f_chiral_restr 0.0475 f_plane_restr 0.0058 f_bond_d 0.0034
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3336 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 35
Software Software Software Name Purpose HKL-2000 data scaling HKL-2000 data reduction PHENIX refinement PHASER phasing