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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, GPC3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.8 291.15 0.1M Tris (pH 7.8)
5% w/v gamma-PGA,
20% w/vPEG 3350
Crystal Properties Matthews coefficient Solvent content 3.18 61.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.577 α = 90 b = 119.577 β = 90 c = 257.936 γ = 120
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 2017-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.80000 Diamond I03
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 80.878 73.8 0.053 0.02 1 12.6 8.2 26038 269.6
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 4.227 0.761 2
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 80.878 26038 1333 74.8 0.357 0.3553 0.3527 0.3846 0.3846 301.314
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] 2.071 1.036 2.071 -6.719
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.398 r_lrange_it 39.988 r_lrange_other 39.988 r_mcangle_it 18.852 r_mcangle_other 18.852 r_dihedral_angle_3_deg 17.758 r_scangle_it 15.027 r_scangle_other 15.026 r_dihedral_angle_4_deg 13.208 r_mcbond_other 10.807
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.398 r_lrange_it 39.988 r_lrange_other 39.988 r_mcangle_it 18.852 r_mcangle_other 18.852 r_dihedral_angle_3_deg 17.758 r_scangle_it 15.027 r_scangle_other 15.026 r_dihedral_angle_4_deg 13.208 r_mcbond_other 10.807 r_mcbond_it 10.806 r_scbond_it 8.141 r_scbond_other 8.141 r_dihedral_angle_1_deg 3.907 r_angle_other_deg 1.485 r_angle_refined_deg 1.375 r_symmetry_nbd_refined 0.715 r_nbd_other 0.559 r_symmetry_xyhbond_nbd_refined 0.508 r_xyhbond_nbd_other 0.324 r_nbd_refined 0.23 r_symmetry_nbd_other 0.209 r_xyhbond_nbd_refined 0.202 r_nbtor_refined 0.171 r_symmetry_xyhbond_nbd_other 0.163 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.067 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 autoPROC data reduction xia2 data scaling PHENIX phasing