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Crystal structure of adaptor protein complex 4 (AP-4) mu4 subunit C-terminal domain, in complex with a sorting peptide from the amyloid precursor protein (APP)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 10% PEG 3350, 10mM magnesium chloride, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K 2 VAPOR DIFFUSION, HANGING DROP 7 295 15% PEG 6000, 3% trimethylamine N-oxide dihydrate, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.672 α = 90 b = 56.91 β = 106.53 c = 60.664 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 CCD MARMOSAIC 300 mm CCD 2009-03-20 M MAD 2 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2009-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.9794, 0.9796, 0.9719 APS 23-ID-D 2 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
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 1,2 1.6 50 97.3 0.097 13.8 4.4 39566 39268 1.48
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 MAD THROUGHOUT 1.6 41.67 39268 1972 97.47 0.209 0.207 0.2034 0.252 0.2488 RANDOM 27.823
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] 0.01 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.233 r_dihedral_angle_4_deg 22.493 r_dihedral_angle_3_deg 14.962 r_dihedral_angle_1_deg 7.632 r_scangle_it 4.817 r_scbond_it 3.087 r_mcangle_it 2.36 r_angle_refined_deg 1.731 r_mcbond_it 1.474 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.233 r_dihedral_angle_4_deg 22.493 r_dihedral_angle_3_deg 14.962 r_dihedral_angle_1_deg 7.632 r_scangle_it 4.817 r_scbond_it 3.087 r_mcangle_it 2.36 r_angle_refined_deg 1.731 r_mcbond_it 1.474 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.249 r_symmetry_hbond_refined 0.22 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.125 r_bond_refined_d 0.015 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2038 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 18
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction