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Crystal Structure of the amyloid-fibril forming peptide GGVVIA derived from the Alzheimer's amyloid Abeta (Abeta37-42).
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 291 Peptide concentration: 15.0 mg/ml, Peptide:reservoir:additive ratio 5:4:1, Reservoir: 2.0M Ammonium sulfate, Additive: 3.0% 0.1M hexamine cobalt (III) chloride , VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.6 23.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 16.76 α = 90 b = 41.134 β = 90 c = 4.789 γ = 90
Symmetry Space Group P 21 21 2
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 2005-12-17 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 1.6 90 96.7 0.192 12.6 4.5 532 15.962
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) 1.6 1.72 96.7 0.42 4.9 87
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 GGVVIA 1.61 20.57 515 51 96.44 0.235 0.228 0.2352 0.299 0.3202 RANDOM 9.99
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] 0.7 0.89 -1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.031 r_angle_refined_deg 1.859 r_mcangle_it 1.773 r_dihedral_angle_3_deg 1.738 r_mcbond_it 1.388 r_angle_other_deg 1.041 r_scangle_it 0.89 r_scbond_it 0.651 r_xyhbond_nbd_refined 0.352 r_symmetry_vdw_other 0.273
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.031 r_angle_refined_deg 1.859 r_mcangle_it 1.773 r_dihedral_angle_3_deg 1.738 r_mcbond_it 1.388 r_angle_other_deg 1.041 r_scangle_it 0.89 r_scbond_it 0.651 r_xyhbond_nbd_refined 0.352 r_symmetry_vdw_other 0.273 r_nbd_other 0.182 r_symmetry_vdw_refined 0.16 r_nbtor_refined 0.158 r_symmetry_hbond_refined 0.148 r_mcbond_other 0.137 r_chiral_restr 0.084 r_nbtor_other 0.078 r_nbd_refined 0.026 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 36 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction