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Structure of the amyloid forming segment, GAVVTGVTAVA, from the NAC domain of Parkinson's disease protein alpha-synuclein, residues 68-78, determined by electron diffraction
1 mg of synthetic peptide GAVVTGVTAVA was dissolved in 1 ml of sterile water and shaken overnight in an orbital mixing plate, pH 4.0, batch crystallization, temperature 310K
Crystal Properties
Matthews coefficient
Solvent content
1.46
15.81
Crystal Data
Unit Cell
Length ( Å )
Angle ( ˚ )
a = 70.81
α = 90
b = 4.82
β = 105.68
c = 16.79
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
electron
100
CMOS
TVIPS F416 CMOS CAMERA
2014-08-28
M
SINGLE WAVELENGTH
Radiation Source
ID #
Source
Type
Wavelength List
Synchrotron Site
Beamline
1
ELECTRON MICROSCOPE
TECNAI F20 TEM
0.0251
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
1.43
16.43
89.9
0.175
5.5
4.4
1073
1073
10.33
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
1.43
1.6
82.5
0.565
2.5
4.4
286
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-Free (Depositor)
R-Free Selection Details
Mean Isotropic B
ELECTRON CRYSTALLOGRAPHY
MOLECULAR REPLACEMENT
THROUGHOUT
4RIK
1.43
16.43
1073
1073
127
87.88
0.2512
0.2512
0.2483
0.275
RANDOM
12.75
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]
-3.9876
-1.5509
3.4908
0.4968
RMS Deviations
Key
Refinement Restraint Deviation
t_other_torsion
6.49
t_omega_torsion
4.08
t_angle_deg
1.65
t_bond_d
0.01
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
RMS Deviations
Key
Refinement Restraint Deviation
t_other_torsion
6.49
t_omega_torsion
4.08
t_angle_deg
1.65
t_bond_d
0.01
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Number
Protein Atoms
66
Nucleic Acid Atoms
Solvent Atoms
2
Heterogen Atoms
Software
Software
Software Name
Purpose
Aimless
data scaling
PHASER
phasing
BUSTER-TNT
refinement
PDB_EXTRACT
data extraction
XDS
data reduction
XSCALE
data scaling
BUSTER
refinement
Sample
amyloid forming segment GAVVTGVTAVA from the NAC domain of alpha-synuclein
Specimen Preparation
Sample Aggregation State
3D ARRAY
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction Method
CRYSTALLOGRAPHY
Data Acquisition
Detector Type
TVIPS TEMCAM-F416 (4k x 4k)
Electron Dose (electrons/Å**2)
0.35
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI TECNAI F20
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode
DIFFRACTION
Specimen Holder Model
GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER