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Crystal structure of Yeast Clathrin Heavy Chain N-terminal domain bound to Epsin-1 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 292 0.2M potassium/sodium tartrate
20%(w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.33 47.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.31 α = 90 b = 56.31 β = 90 c = 254.6 γ = 90
Symmetry Space Group P 43 21 2
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 EIGER X 16M 2022-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.74 127.3 100 0.068 0.071 0.019 1 27.2 26 43582
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 2.019 2.092 0.545 0.843 27.5
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 1.74 63.731 43435 2118 99.942 0.187 0.1853 0.186 0.2299 0.2295 39.413
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] 0.916 0.916 -1.832
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.05 r_dihedral_angle_3_deg 11.701 r_dihedral_angle_1_deg 7.451 r_dihedral_angle_2_deg 6.658 r_lrange_it 6.607 r_lrange_other 6.463 r_scangle_it 4.281 r_scangle_other 4.28 r_mcangle_it 3.437 r_mcangle_other 3.437
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.05 r_dihedral_angle_3_deg 11.701 r_dihedral_angle_1_deg 7.451 r_dihedral_angle_2_deg 6.658 r_lrange_it 6.607 r_lrange_other 6.463 r_scangle_it 4.281 r_scangle_other 4.28 r_mcangle_it 3.437 r_mcangle_other 3.437 r_scbond_it 2.826 r_scbond_other 2.825 r_mcbond_it 2.337 r_mcbond_other 2.336 r_angle_refined_deg 1.687 r_angle_other_deg 0.573 r_nbd_other 0.224 r_symmetry_nbd_other 0.193 r_nbd_refined 0.192 r_xyhbond_nbd_refined 0.187 r_nbtor_refined 0.174 r_symmetry_nbd_refined 0.164 r_symmetry_xyhbond_nbd_refined 0.162 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.085 r_symmetry_xyhbond_nbd_other 0.031 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2995 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing