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Crystal Structure of the GULP1 PTB domain-APP peptide complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NTV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.3 289.15 100 mM Glycine (pH3.3), 2000 mM (NH4)2SO4, 50 mM NaCl and 50 mM KCl
Crystal Properties Matthews coefficient Solvent content 3.06 59.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.91 α = 90 b = 63.91 β = 90 c = 108.771 γ = 120
Symmetry Space Group P 32 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 110 IMAGE PLATE RIGAKU RAXIS IV++ 2011-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5419
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 2.17 32 98.4 0.056 26.8 5.3 13797
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 2.17 2.29 0.369
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 1NTV 2.17 32 13107 688 97.57 0.19779 0.19656 0.2067 0.22081 0.2256 RANDOM 56.312
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] -0.05 -0.03 -0.05 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.307 r_dihedral_angle_3_deg 14.556 r_dihedral_angle_4_deg 10.518 r_long_range_B_refined 10.039 r_long_range_B_other 10.037 r_dihedral_angle_1_deg 7.728 r_scangle_other 7.657 r_mcangle_other 5.625 r_mcangle_it 5.623 r_scbond_it 5.492
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.307 r_dihedral_angle_3_deg 14.556 r_dihedral_angle_4_deg 10.518 r_long_range_B_refined 10.039 r_long_range_B_other 10.037 r_dihedral_angle_1_deg 7.728 r_scangle_other 7.657 r_mcangle_other 5.625 r_mcangle_it 5.623 r_scbond_it 5.492 r_scbond_other 5.49 r_mcbond_it 4.114 r_mcbond_other 4.105 r_angle_refined_deg 1.678 r_angle_other_deg 0.974 r_chiral_restr 0.094 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1284 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALEPACK data scaling PHASER phasing