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Crystal structure of the alpha-adaptin appendage domain, from the AP2 adaptor complex, bound to 2 peptides from Synaptojanin170
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 SULFATE, 3% ISOPROPANOL, 0.05M SODIUM CITRATE, pH 6.50
Crystal Properties Matthews coefficient Solvent content 3.6 65.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.599 α = 90 b = 67.322 β = 94.53 c = 39.721 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 MIRROR 2004-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.9 70 95.1 0.08 0.09 12.1 3.4 28939 27.28
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 73.7 0.65 0.87 1.8 2.1
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 1.9 72.55 27464 1467 95 0.179 0.177 0.188 0.224 0.2347 RANDOM 27.98
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] 1.63 -0.89 0.44 -2.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.184 r_dihedral_angle_4_deg 15.341 r_dihedral_angle_3_deg 13.341 r_dihedral_angle_1_deg 6.701 r_scangle_it 5.076 r_scbond_it 3.644 r_mcangle_it 2.246 r_angle_refined_deg 2.238 r_mcbond_it 1.927 r_angle_other_deg 1.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.184 r_dihedral_angle_4_deg 15.341 r_dihedral_angle_3_deg 13.341 r_dihedral_angle_1_deg 6.701 r_scangle_it 5.076 r_scbond_it 3.644 r_mcangle_it 2.246 r_angle_refined_deg 2.238 r_mcbond_it 1.927 r_angle_other_deg 1.013 r_symmetry_vdw_other 0.295 r_xyhbond_nbd_refined 0.246 r_nbd_refined 0.232 r_symmetry_vdw_refined 0.194 r_symmetry_hbond_refined 0.192 r_nbd_other 0.19 r_nbtor_refined 0.184 r_chiral_restr 0.132 r_nbtor_other 0.093 r_bond_refined_d 0.029 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 2096 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing