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AP2 Mu2 adaptin C-terminal domain complexed with integrin alpha-4 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BXX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.1 293 2.2M NaCl, 0.4M Na/K phosphate, 10MM DTT 0.1M MES pH 7.1, 15% glycerol, molar ratio of peptide to protein 3:1
Crystal Properties Matthews coefficient Solvent content 5.6 77.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.65 α = 90 b = 125.65 β = 90 c = 74.41 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 IMAGE PLATE MAR scanner 345 mm plate 2014-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E DW 1.54182
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 2.75 74 97.2 0.062 0.062 14.2 4.9 17034 17034
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 2.75 2.9 80.8 0.325 3.7 4.6
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 (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 1bxx 2.77 74 17008 893 99.26 0.1768 0.1743 0.1819 0.2243 0.2277 RANDOM 61.7828
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] -0.44 -0.22 -0.44 1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.066 r_dihedral_angle_4_deg 22.817 r_dihedral_angle_3_deg 20.607 r_dihedral_angle_1_deg 8.409 r_mcangle_it 7.868 r_mcbond_it 5.488 r_mcbond_other 5.486 r_angle_other_deg 3.547 r_angle_refined_deg 2.084 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.066 r_dihedral_angle_4_deg 22.817 r_dihedral_angle_3_deg 20.607 r_dihedral_angle_1_deg 8.409 r_mcangle_it 7.868 r_mcbond_it 5.488 r_mcbond_other 5.486 r_angle_other_deg 3.547 r_angle_refined_deg 2.084 r_chiral_restr 0.109 r_bond_refined_d 0.019 r_gen_planes_other 0.013 r_gen_planes_refined 0.009 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2130 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms
Software Software Software Name Purpose PDB_EXTRACT data extraction MOSFLM data reduction Aimless data scaling PHASER phasing REFMAC refinement