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MVGGVV peptide derived from Alzheimer's A-beta, residues 35-40
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other polyalanine idealized beta strand
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 30 mg/mL peptide in water mixed 1:1 with reservoir containing 0.02 M CaCl2, 30% MPD, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 25.862 α = 77.18 b = 9.699 β = 74.69 c = 15.851 γ = 86.93
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 2005-12-18 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 2 90 90.2 0.16 10.2 1.6 409 -3 25.4
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) 2 2.15 94.2 0.222 1.6 163
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 polyalanine idealized beta strand 2.03 24.94 409 44 0.211 0.202 0.2054 0.264 0.286 RANDOM 10.788
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] -0.1 -0.28 0.26 0.1 -0.07 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.457 r_scangle_it 2.628 r_dihedral_angle_1_deg 2.56 r_scbond_it 2.08 r_mcangle_it 1.821 r_mcbond_it 1.732 r_angle_refined_deg 1.254 r_angle_other_deg 0.669 r_mcbond_other 0.456 r_symmetry_vdw_refined 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.457 r_scangle_it 2.628 r_dihedral_angle_1_deg 2.56 r_scbond_it 2.08 r_mcangle_it 1.821 r_mcbond_it 1.732 r_angle_refined_deg 1.254 r_angle_other_deg 0.669 r_mcbond_other 0.456 r_symmetry_vdw_refined 0.23 r_nbd_other 0.18 r_symmetry_vdw_other 0.177 r_nbd_refined 0.159 r_xyhbond_nbd_refined 0.145 r_nbtor_refined 0.14 r_symmetry_hbond_refined 0.096 r_nbtor_other 0.085 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 152 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction