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Clathrin terminal domain complexed with C-terminus of AAK1L
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UTC 1UTC_1 (chain A/B)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293.15 20% PEG 3,350; 100 mM Bis-Tris propane, pH 6.0; 200 mM sodium citrate; 10 mM DTT
Crystal Properties Matthews coefficient Solvent content 3.24 62.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.539 α = 90 b = 130.86 β = 90 c = 77.05 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 100 PIXEL DECTRIS PILATUS 6M 2016-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 1.71 28.3 95.47 0.0686 0.097 0.0686 0.987 4.83 1.87 56178
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 1.71 1.77 88.8 0.452 0.64 0.452 0.603 1.15 1.83
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 1.711 28.264 56177 2770 95.473 0.174 0.1723 0.1815 0.2092 0.2182 24.229
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] 0.466 0.588 -1.054
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.734 r_dihedral_angle_3_deg 12.247 r_dihedral_angle_2_deg 12.123 r_lrange_it 8.051 r_lrange_other 7.84 r_dihedral_angle_1_deg 7.238 r_scangle_it 5.962 r_scangle_other 5.961 r_mcangle_other 3.843 r_mcangle_it 3.837
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.734 r_dihedral_angle_3_deg 12.247 r_dihedral_angle_2_deg 12.123 r_lrange_it 8.051 r_lrange_other 7.84 r_dihedral_angle_1_deg 7.238 r_scangle_it 5.962 r_scangle_other 5.961 r_mcangle_other 3.843 r_mcangle_it 3.837 r_scbond_it 3.805 r_scbond_other 3.804 r_mcbond_it 2.538 r_mcbond_other 2.529 r_angle_refined_deg 1.677 r_angle_other_deg 0.906 r_symmetry_xyhbond_nbd_refined 0.254 r_symmetry_nbd_other 0.213 r_nbd_refined 0.199 r_nbd_other 0.179 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.174 r_symmetry_nbd_refined 0.169 r_symmetry_nbtor_other 0.093 r_chiral_restr 0.087 r_gen_planes_other 0.011 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2933 Nucleic Acid Atoms Solvent Atoms 384 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing