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Clathrin heavy chain N-terminal domain bound to amphiphysin clathrin-box motif
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, SITTING DROP 7.5 293 1 uL protein:peptide mix (14 mg/mL NTD and 3.4 mM peptide) plus 2 uL reservoir equilibrated against a 200 uL reservoir of 0.85 M sodium malonate pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.87 68.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.967 α = 90 b = 134.11 β = 115.07 c = 78.012 γ = 90
Symmetry Space Group C 1 2 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 PILATUS 6M-F toroidal mirrors 2015-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
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 1.88 67.1 100 0.149 0.993 6.5 5.1 99868
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.93 100 1.092 0.568 1.3 4.4
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 1.88 67.06 99868 5291 99.5 0.20565 0.20418 0.2111 0.23388 0.2388 RANDOM 23.627
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] 0.4 -0.25 -0.87 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.388 r_dihedral_angle_4_deg 13.984 r_dihedral_angle_3_deg 13.091 r_long_range_B_refined 8.134 r_long_range_B_other 8.134 r_dihedral_angle_1_deg 6.286 r_angle_refined_deg 1.396 r_mcangle_it 1.346 r_mcangle_other 1.345 r_scangle_other 0.974
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.388 r_dihedral_angle_4_deg 13.984 r_dihedral_angle_3_deg 13.091 r_long_range_B_refined 8.134 r_long_range_B_other 8.134 r_dihedral_angle_1_deg 6.286 r_angle_refined_deg 1.396 r_mcangle_it 1.346 r_mcangle_other 1.345 r_scangle_other 0.974 r_angle_other_deg 0.9 r_mcbond_it 0.732 r_mcbond_other 0.731 r_scbond_it 0.515 r_scbond_other 0.515 r_chiral_restr 0.09 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5890 Nucleic Acid Atoms Solvent Atoms 803 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing