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Crystal structure of clathrin heavy chain in complex with a peptidomimetic inhibitor of the TACC3 interaction
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ODS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 291 20% w/v polyethylene glycol 3350
200 mM tri-potassium citrate
Crystal Properties Matthews coefficient Solvent content 2.96 58.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.218 α = 90 b = 111.218 β = 90 c = 212.862 γ = 120
Symmetry Space Group P 61 2 2
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 2023-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95373 Diamond I04
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 2.146 96.318 96.1 0.984 23 39.5 24209
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 2.146 2.419 0.785
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.146 96.318 24209 1204 55.9 0.207 0.2036 0.2039 0.2684 0.2683 63.272
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] 0.011 0.005 0.011 -0.035
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.468 r_dihedral_angle_3_deg 16.839 r_dihedral_angle_6_deg 15.358 r_lrange_it 11.435 r_scangle_it 8.332 r_dihedral_angle_1_deg 7.51 r_mcangle_it 6.329 r_scbond_it 5.639 r_mcbond_it 4.04 r_angle_refined_deg 2.284
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.468 r_dihedral_angle_3_deg 16.839 r_dihedral_angle_6_deg 15.358 r_lrange_it 11.435 r_scangle_it 8.332 r_dihedral_angle_1_deg 7.51 r_mcangle_it 6.329 r_scbond_it 5.639 r_mcbond_it 4.04 r_angle_refined_deg 2.284 r_nbtor_refined 0.315 r_nbd_refined 0.24 r_symmetry_nbd_refined 0.227 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.134 r_symmetry_xyhbond_nbd_refined 0.104 r_bond_refined_d 0.011 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4629 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing