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MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH LRP6 INTERNALIZATION PEPTIDE SYRHFA
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 5.25 76.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.625 α = 90 b = 127.625 β = 90 c = 75.08 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 0.928190 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.82 48.67 99.9 0.07 0.022 30.1 20.3 17042
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.82 2.97 1.58 0.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.82 48.67 16168 850 99.89 0.19454 0.19197 0.201 0.2457 0.2456 RANDOM 93.824
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] -0.22 -0.11 -0.22 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.397 r_long_range_B_other 16.437 r_long_range_B_refined 16.432 r_scangle_other 14.021 r_mcangle_other 11.359 r_mcangle_it 11.357 r_scbond_it 10.162 r_scbond_other 10.16 r_dihedral_angle_1_deg 9.536 r_mcbond_other 8.574
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.397 r_long_range_B_other 16.437 r_long_range_B_refined 16.432 r_scangle_other 14.021 r_mcangle_other 11.359 r_mcangle_it 11.357 r_scbond_it 10.162 r_scbond_other 10.16 r_dihedral_angle_1_deg 9.536 r_mcbond_other 8.574 r_mcbond_it 8.573 r_dihedral_angle_2_deg 7.549 r_angle_refined_deg 1.908 r_angle_other_deg 0.628 r_chiral_restr 0.087 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 2068 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling