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Structure of an amyloid forming peptide VQIVYK from the repeat region of Tau
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other geometrically idealized b-strands
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 Peptide concentration: 30mg/ml, peptide:Reservoir ratio 1:1, Reservoir: 0.2M Ammonium acetate, 0.1M HEPES-Na, 45% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.53 19.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 4.863 α = 90 b = 61.926 β = 98.11 c = 15.413 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 MAR CCD 165 mm 2005-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID13 ESRF ID13
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 1.5 90 85.4 0.161 3.8 2.89 1222
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) 1.5 1.62 77 0.489 238
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 Extended beta strand VQIVYK 1.51 30.96 1207 59 85.06 0.207 0.206 0.2127 0.225 0.2091 RANDOM 8.391
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] 0.08 0.03 -0.14 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.032 r_dihedral_angle_3_deg 11.4 r_dihedral_angle_1_deg 4.252 r_scangle_it 1.332 r_angle_refined_deg 1.197 r_scbond_it 1.11 r_mcangle_it 0.761 r_angle_other_deg 0.757 r_mcbond_it 0.62 r_xyhbond_nbd_refined 0.239
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.032 r_dihedral_angle_3_deg 11.4 r_dihedral_angle_1_deg 4.252 r_scangle_it 1.332 r_angle_refined_deg 1.197 r_scbond_it 1.11 r_mcangle_it 0.761 r_angle_other_deg 0.757 r_mcbond_it 0.62 r_xyhbond_nbd_refined 0.239 r_nbtor_refined 0.183 r_nbd_other 0.178 r_symmetry_vdw_other 0.177 r_symmetry_hbond_refined 0.143 r_mcbond_other 0.122 r_symmetry_vdw_refined 0.121 r_chiral_restr 0.092 r_nbtor_other 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_nbd_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 111 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction