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MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH LRP6 INTERNALIZATION PEPTIDE SYRPYSYRHFA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BW8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 2.0-2.2 M NaCl
0.4M Na/K phosphate
0.1M MES PH 7.1
15-20% glycerol
Crystal Properties Matthews coefficient Solvent content 4.91 74.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.796 α = 90 b = 125.796 β = 90 c = 73.766 γ = 120
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 12M 2017-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9677 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.78 47.91 99.7 0.11 0.11 0.035 19.8 20.8 16878
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.78 2.93 1.75 1.84 0.56 2.1
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.78 47.91 16018 842 99.53 0.19843 0.19662 0.23342 0.2245 RANDOM 87.539
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] 0.18 0.09 0.18 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.861 r_long_range_B_refined 16.943 r_long_range_B_other 16.941 r_scangle_other 14.036 r_mcangle_other 11.293 r_mcangle_it 11.289 r_dihedral_angle_2_deg 10.453 r_scbond_it 9.9 r_scbond_other 9.897 r_dihedral_angle_1_deg 9.281
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.861 r_long_range_B_refined 16.943 r_long_range_B_other 16.941 r_scangle_other 14.036 r_mcangle_other 11.293 r_mcangle_it 11.289 r_dihedral_angle_2_deg 10.453 r_scbond_it 9.9 r_scbond_other 9.897 r_dihedral_angle_1_deg 9.281 r_mcbond_other 8.314 r_mcbond_it 8.313 r_angle_refined_deg 1.884 r_angle_other_deg 0.616 r_chiral_restr 0.082 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 2089 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling