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Vvtgvta, an amyloid forming segment from alpha synuclein, residues 70-76
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other ideal beta strand
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 isopropanol, sodium cacodylate, pH 6.5, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.4 12.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.367 α = 90 b = 4.823 β = 107.89 c = 15.692 γ = 90
Symmetry Space Group C 1 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 100 CCD MAR CCD 165 mm 2007-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID13 0.895432 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 93.9 0.193 5 3.1 650 650 -3 17.4
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) 1 1.5 1.62 88.3 0.177 2.3 121
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 ideal beta strand 1.5 23.97 648 648 62 93.51 0.2467 0.2467 0.244 0.262 0.2739 0.2848 RANDOM 11.91
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] 0.37 0.53 -3 2.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 6.614 r_dihedral_angle_1_deg 3.33 r_mcangle_it 2.981 r_mcbond_it 2.408 r_scbond_it 1.568 r_angle_refined_deg 1.432 r_scangle_it 1.124 r_angle_other_deg 0.873 r_mcbond_other 0.371 r_nbd_other 0.248
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 6.614 r_dihedral_angle_1_deg 3.33 r_mcangle_it 2.981 r_mcbond_it 2.408 r_scbond_it 1.568 r_angle_refined_deg 1.432 r_scangle_it 1.124 r_angle_other_deg 0.873 r_mcbond_other 0.371 r_nbd_other 0.248 r_symmetry_vdw_other 0.213 r_nbtor_refined 0.17 r_symmetry_hbond_refined 0.155 r_nbtor_other 0.097 r_chiral_restr 0.087 r_symmetry_vdw_refined 0.07 r_nbd_refined 0.064 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 45 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction