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The complex structure of PHF core domain peptide of tau, VQIVYK, and antibody's Fab domain.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LRA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 19% PEG3350, 20% Glycerol, 0.2M Ammonium iodide, 0.01M Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.62 53.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.98 α = 90 b = 70.72 β = 90 c = 118.03 γ = 90
Symmetry Space Group P 21 21 21
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 RIGAKU RAXIS VII 2019-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 1.5406
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 1.9 59.08 99.4 0.06 10.6 3.47 28351
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 1.9 1.97 0.364
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 6LRA 2.1 59.08 28351 1518 99.44 0.20317 0.1997 0.2085 0.26962 0.2788 RANDOM 36.22
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] 0.71 -0.49 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.566 r_dihedral_angle_3_deg 15.275 r_dihedral_angle_4_deg 12.948 r_dihedral_angle_1_deg 8.764 r_long_range_B_refined 6.367 r_long_range_B_other 6.366 r_scangle_other 4.264 r_mcangle_it 3.988 r_mcangle_other 3.987 r_scbond_it 2.841
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.566 r_dihedral_angle_3_deg 15.275 r_dihedral_angle_4_deg 12.948 r_dihedral_angle_1_deg 8.764 r_long_range_B_refined 6.367 r_long_range_B_other 6.366 r_scangle_other 4.264 r_mcangle_it 3.988 r_mcangle_other 3.987 r_scbond_it 2.841 r_scbond_other 2.84 r_mcbond_it 2.692 r_mcbond_other 2.69 r_angle_refined_deg 1.539 r_angle_other_deg 1.223 r_chiral_restr 0.065 r_bond_refined_d 0.007 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 3344 Nucleic Acid Atoms Solvent Atoms 422 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction CrystalClear data scaling BALBES phasing Coot model building PDB_EXTRACT data extraction