4RIL | pdb_00004ril

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

ELECTRON CRYSTALLOGRAPHY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4RIK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	batch crystallization	4	310	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
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
Nominal Magnification
Calibrated Magnification
Source
Acceleration Voltage (kV)	200
Imaging Details