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Crystal structure of the alpha-adaptin appendage domain, from the AP2 adaptor complex, in complex with an FXDNF peptide from amphiphysin1 and a WVXF peptide from synaptojanin P170
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B9K PDB ENTRY 1B9K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 1.2M AMMONIUM SULPHATE, 3% ISOPROPANOL AND 0.05M SODIUM CITRATE PH 6.5
Crystal Properties Matthews coefficient Solvent content 3.2 61.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.508 α = 90 b = 66.98 β = 94.92 c = 39.73 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 CCD ADSC CCD BENT MIRRORS 2004-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 SRS PX9.6
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.6 17.76 96.3 0.08 10.8 2.7 47896 2 17.59
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.69 89.2 0.37 2 2.4
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 PDB ENTRY 1B9K 1.6 17.76 47892 2427 96.2 0.182 0.181 0.1924 0.208 0.2192 RANDOM 16.14
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] 0.205 0.164 -0.34 0.164
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.269 r_dihedral_angle_4_deg 16.453 r_dihedral_angle_3_deg 11.206 r_dihedral_angle_1_deg 6.099 r_scangle_it 3.362 r_scbond_it 2.197 r_mcangle_it 1.426 r_angle_refined_deg 1.299 r_mcbond_it 1.001 r_nbd_refined 0.202
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.269 r_dihedral_angle_4_deg 16.453 r_dihedral_angle_3_deg 11.206 r_dihedral_angle_1_deg 6.099 r_scangle_it 3.362 r_scbond_it 2.197 r_mcangle_it 1.426 r_angle_refined_deg 1.299 r_mcbond_it 1.001 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.18 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.151 r_symmetry_hbond_refined 0.126 r_chiral_restr 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other 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 343 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing