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GPC3-Unc5D octamer structure and role in cell migration
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FTT 5FTT, hGPC3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 291.15 20% ethylene glycol,
10% w/v PEG 8000,
0.1 M Tris/BICINE (pH 8.5)
and 0.02 M of amino acids (L-Na-glutamate, alanine, glycine, lysine-HCl, and serine)
Crystal Properties Matthews coefficient Solvent content 2.98 58.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.643 α = 90 b = 157.584 β = 102.949 c = 126.601 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 PIXEL DECTRIS PILATUS 6M-F 2018-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 4.1 123.4 73 0.109 0.13 0.071 0.994 3.4 3.4 22459 143.4
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 4.1 4.55 10.9 0.738 1.6 3.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5FTT, hGPC3 4.1 97.336 18399 899 59.546 0.326 0.3239 0.3231 0.3648 0.3645 186.258
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] 0.883 1.725 3.2 -4.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.776 r_lrange_it 17.238 r_lrange_other 17.238 r_dihedral_angle_3_deg 16.034 r_dihedral_angle_4_deg 12.084 r_mcangle_it 6.562 r_mcangle_other 6.562 r_scangle_it 5.457 r_scangle_other 5.457 r_mcbond_it 3.643
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.776 r_lrange_it 17.238 r_lrange_other 17.238 r_dihedral_angle_3_deg 16.034 r_dihedral_angle_4_deg 12.084 r_mcangle_it 6.562 r_mcangle_other 6.562 r_scangle_it 5.457 r_scangle_other 5.457 r_mcbond_it 3.643 r_mcbond_other 3.642 r_dihedral_angle_1_deg 3.233 r_scbond_it 2.882 r_scbond_other 2.882 r_angle_refined_deg 1.572 r_angle_other_deg 1.556 r_symmetry_nbd_refined 0.345 r_nbd_other 0.309 r_nbd_refined 0.235 r_xyhbond_nbd_refined 0.228 r_symmetry_nbd_other 0.214 r_nbtor_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.108 r_chiral_restr 0.079 r_symmetry_nbtor_other 0.079 r_symmetry_xyhbond_nbd_other 0.032 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19184 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 462
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction xia2 data scaling PHENIX phasing