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AP2 clathrin adaptor core in complex with cargo peptide and FCHO2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XA7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 Crystals of AP-2 in complex with FCHO2 linker and TGN38 peptide, supplemented with 10mM K Na Tartrate, grew in sitting drops with reservoir 0.1M Mg formate dehydrate, 10% to 15% PEG 3350.
The crystals were cryo-protected with 0.1M Mg formate dehydrate, 13% PEG 3350, 18-24% Glycerol and 1mg/ml of peptide.
Crystal Properties Matthews coefficient Solvent content 2.56 51.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.576 α = 90 b = 150.07 β = 112.652 c = 96.43 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 PILATUS3 6M 2017-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.92001 Diamond I04
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 3.25 78.58 100 0.133 0.159 0.086 0.998 7.2 6.6 38355
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 3.25 3.39 100 2.123 2.59 1.465 0.366 0.8 6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2xa7 3.25 76.662 38326 1881 99.924 0.212 0.2066 0.2095 0.3063 0.3013 135.397
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] -2.812 3.095 -4.448 3.469
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.559 r_lrange_it 23.935 r_lrange_other 23.935 r_dihedral_angle_3_deg 22.635 r_mcangle_it 18.686 r_mcangle_other 18.685 r_scangle_it 17.117 r_scangle_other 17.116 r_dihedral_angle_4_deg 15.69 r_mcbond_it 12.128
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.559 r_lrange_it 23.935 r_lrange_other 23.935 r_dihedral_angle_3_deg 22.635 r_mcangle_it 18.686 r_mcangle_other 18.685 r_scangle_it 17.117 r_scangle_other 17.116 r_dihedral_angle_4_deg 15.69 r_mcbond_it 12.128 r_mcbond_other 12.126 r_scbond_it 10.82 r_scbond_other 10.819 r_dihedral_angle_1_deg 9.291 r_angle_refined_deg 1.578 r_angle_other_deg 1.115 r_symmetry_nbd_refined 0.261 r_nbd_refined 0.241 r_nbd_other 0.206 r_symmetry_nbd_other 0.199 r_xyhbond_nbd_refined 0.196 r_nbtor_refined 0.171 r_symmetry_nbtor_other 0.079 r_symmetry_xyhbond_nbd_other 0.071 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_symmetry_xyhbond_nbd_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14392 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHASER phasing PHENIX refinement Aimless data scaling DIALS data reduction