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Clathrin N-terminal domain in complex with a HURP phospho-peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C9I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 50 mM Tris pH 7.5, 30 % PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.4 48.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.774 α = 90 b = 94.242 β = 103.81 c = 88.981 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 100 PIXEL DECTRIS EIGER X 16M 2021-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.87313 ESRF ID23-1
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 2.08 43.2 96 0.099 0.123 0.071 0.909 6.9 2.7 45105
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 2.08 2.12 97.7 0.39 0.475 0.268 0.716 1.3 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1C9I 2.08 43.2 42817 2286 95.99 0.2084 0.2061 0.2139 0.249 0.251 RANDOM 28.039
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] -0.08 0.27 0.38 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.574 r_dihedral_angle_4_deg 17.764 r_dihedral_angle_3_deg 13.963 r_dihedral_angle_1_deg 7.736 r_angle_refined_deg 1.44 r_angle_other_deg 1.233 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.574 r_dihedral_angle_4_deg 17.764 r_dihedral_angle_3_deg 13.963 r_dihedral_angle_1_deg 7.736 r_angle_refined_deg 1.44 r_angle_other_deg 1.233 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5791 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction DIALS data scaling PHASER phasing