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Crystal structure of Yeast Clathrin Heavy Chain N-terminal domain bound to Epsin-5 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 9 292 10 %(w/v) PEG 1000
10 %(w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.77 55.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.995 α = 90 b = 133.449 β = 90 c = 285.527 γ = 90
Symmetry Space Group C 2 2 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 2020-05-19 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 2.01 142.76 95.9 0.12 0.13 0.049 0.999 15.1 12.9 93922
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 2.01 2.05 0.692 0.871 0.517 0.533 3.5
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 2.011 71.484 93850 4607 95.872 0.184 0.1819 0.1829 0.2146 0.2166 42.867
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] 1.351 1.152 -2.503
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.346 r_dihedral_angle_6_deg 13.745 r_dihedral_angle_3_deg 12.065 r_dihedral_angle_1_deg 6.795 r_lrange_it 6.548 r_lrange_other 6.501 r_scangle_it 5.237 r_scangle_other 5.236 r_scbond_it 3.429 r_scbond_other 3.428
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.346 r_dihedral_angle_6_deg 13.745 r_dihedral_angle_3_deg 12.065 r_dihedral_angle_1_deg 6.795 r_lrange_it 6.548 r_lrange_other 6.501 r_scangle_it 5.237 r_scangle_other 5.236 r_scbond_it 3.429 r_scbond_other 3.428 r_mcangle_it 2.968 r_mcangle_other 2.967 r_mcbond_it 2.149 r_mcbond_other 2.149 r_angle_refined_deg 1.428 r_angle_other_deg 0.458 r_nbd_other 0.247 r_nbd_refined 0.185 r_symmetry_nbd_other 0.185 r_symmetry_xyhbond_nbd_refined 0.175 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.161 r_symmetry_nbd_refined 0.132 r_symmetry_nbtor_other 0.082 r_ncsr_local_group_2 0.079 r_ncsr_local_group_1 0.075 r_ncsr_local_group_3 0.067 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_chiral_restr_other 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8901 Nucleic Acid Atoms Solvent Atoms 604 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing