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Crystal structure of Yeast Clathrin Heavy Chain N-terminal domain bound to Epsin-2 peptide (LIDL)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9EXF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 292 0.2M Lithium sulfate
0.1M Bis-Tris pH 5.5
25% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.28 46.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.496 α = 90 b = 94.289 β = 90 c = 269.026 γ = 90
Symmetry Space Group P 21 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 196 PIXEL DECTRIS EIGER2 X 16M 2022-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9763 PETRA III, EMBL c/o DESY P14 (MX2)
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 1.74 67.347 99.9 0.09 0.097 0.037 0.999 16.7 13.1 121808
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.74 1.77 1.102 1.194 0.457 0.788 12.9
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.744 67.347 121660 6253 99.837 0.193 0.1913 0.2261 0.2151 32.856
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] 4.231 -2.74 -1.491
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.565 r_dihedral_angle_6_deg 15.921 r_dihedral_angle_3_deg 13.205 r_dihedral_angle_1_deg 6.067 r_lrange_it 4.047 r_lrange_other 3.98 r_angle_refined_deg 1.532 r_scangle_it 1.245 r_scangle_other 1.243 r_mcangle_it 0.945
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.565 r_dihedral_angle_6_deg 15.921 r_dihedral_angle_3_deg 13.205 r_dihedral_angle_1_deg 6.067 r_lrange_it 4.047 r_lrange_other 3.98 r_angle_refined_deg 1.532 r_scangle_it 1.245 r_scangle_other 1.243 r_mcangle_it 0.945 r_mcangle_other 0.945 r_scbond_it 0.806 r_scbond_other 0.799 r_mcbond_it 0.585 r_mcbond_other 0.585 r_angle_other_deg 0.5 r_symmetry_nbd_refined 0.245 r_nbd_other 0.217 r_nbd_refined 0.196 r_symmetry_nbd_other 0.189 r_symmetry_xyhbond_nbd_refined 0.179 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.155 r_ncsr_local_group_3 0.135 r_ncsr_local_group_1 0.132 r_ncsr_local_group_2 0.128 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.075 r_symmetry_xyhbond_nbd_other 0.016 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8921 Nucleic Acid Atoms Solvent Atoms 929 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing