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Crystal structure of Yeast Clathrin Heavy Chain N-terminal domain bound to YAP1801 peptide (LIDM)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other PHYRE2 generated homology model of ScCHC-NTD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 292 0.1M TRIS-HCl pH 8.5
0.28182M Lithium Sfate monohydrate
30% (w/v) PEG4000
Crystal Properties Matthews coefficient Solvent content 2.55 51.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.083 α = 90 b = 89.739 β = 90.392 c = 188.122 γ = 90
Symmetry Space Group P 1 21 1
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 2019-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9793 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.95 81 95.3 0.108 0.998 11 7.7 116855
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 1.98 86.3 1.242 0.553 0.499 1.5 7.1
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 1.95 65.013 116848 5916 94.399 0.183 0.1814 0.1815 0.212 0.2121 37.123
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] 0.427 0.109 -0.182 -0.246
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.437 r_dihedral_angle_3_deg 13.827 r_dihedral_angle_2_deg 10.653 r_dihedral_angle_1_deg 6.691 r_lrange_it 5.944 r_lrange_other 5.915 r_scangle_it 4.061 r_scangle_other 4.061 r_scbond_it 2.592 r_scbond_other 2.592
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.437 r_dihedral_angle_3_deg 13.827 r_dihedral_angle_2_deg 10.653 r_dihedral_angle_1_deg 6.691 r_lrange_it 5.944 r_lrange_other 5.915 r_scangle_it 4.061 r_scangle_other 4.061 r_scbond_it 2.592 r_scbond_other 2.592 r_mcangle_it 2.529 r_mcangle_other 2.529 r_mcbond_it 1.655 r_mcbond_other 1.655 r_angle_refined_deg 1.517 r_angle_other_deg 0.499 r_symmetry_xyhbond_nbd_other 0.193 r_nbd_refined 0.188 r_symmetry_nbd_other 0.187 r_nbd_other 0.17 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.159 r_symmetry_xyhbond_nbd_refined 0.151 r_symmetry_nbd_refined 0.147 r_ncsr_local_group_6 0.101 r_ncsr_local_group_2 0.097 r_ncsr_local_group_1 0.095 r_ncsr_local_group_4 0.093 r_ncsr_local_group_5 0.09 r_ncsr_local_group_3 0.086 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.071 r_bond_refined_d 0.007 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 11928 Nucleic Acid Atoms Solvent Atoms 614 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing