☰ Navigation Tabs
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, GPC3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 291.15 15% w/v PEG 3000, 20% v/v 1, 2, 4-butanetrol, 1% w/v NDSB 256, 0.1 M Gly-GLy/AMPD (pH 8.5) and 0.2 M of amino acids (DL-arginine HCL, DL-threonine, DL-histidine HCL H2O, DL-5-hydroxylysine HCL, trans-4-hydroxyl-L-proline).
Crystal Properties Matthews coefficient Solvent content 2.98 58.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.113 α = 90 b = 157.994 β = 102.91 c = 126.572 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 EIGER2 XE 16M 2018-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 4.6 66.62 99.7 0.09281 0.03962 0.997 7.77 6.6 21870 245.99
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 4.6 4.76 0.485 1.81
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, GPC3 4.6 66.616 21812 1866 99.621 0.311 0.3075 0.3089 0.347 0.3498 331.565
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] 15.254 9.105 -7.738 -10.578
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.361 r_lrange_it 34.816 r_lrange_other 34.816 r_dihedral_angle_3_deg 17.498 r_mcangle_it 16.75 r_mcangle_other 16.749 r_scangle_it 15.207 r_scangle_other 15.207 r_dihedral_angle_4_deg 13.212 r_mcbond_it 9.703
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.361 r_lrange_it 34.816 r_lrange_other 34.816 r_dihedral_angle_3_deg 17.498 r_mcangle_it 16.75 r_mcangle_other 16.749 r_scangle_it 15.207 r_scangle_other 15.207 r_dihedral_angle_4_deg 13.212 r_mcbond_it 9.703 r_mcbond_other 9.701 r_scbond_it 8.308 r_scbond_other 8.307 r_dihedral_angle_1_deg 3.74 r_angle_other_deg 1.521 r_angle_refined_deg 1.384 r_symmetry_nbd_refined 0.325 r_nbd_other 0.312 r_nbd_refined 0.228 r_symmetry_nbd_other 0.209 r_xyhbond_nbd_refined 0.2 r_nbtor_refined 0.173 r_symmetry_xyhbond_nbd_other 0.138 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19188 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 257
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHENIX phasing