4ZNN | pdb_00004znn

MicroED structure of the segment, GVVHGVTTVA, from the A53T familial mutant of Parkinson's disease protein, alpha-synuclein residues 47-56

ELECTRON CRYSTALLOGRAPHY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	7	310	1 mg of synthetic peptide GVVHGVTTVA was dissolved in 200 microliters of 50 mM phosphate buffer pH 7.0 and 0.1% w/v DMSO and shaken overnight in an orbital mixing plate

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 17.93	α = 90
b = 4.71	β = 94.33
c = 33.03	γ = 90

Symmetry
Space Group	P 1 21 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			2015-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ELECTRON MICROSCOPE	OTHER	0.0251

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.41	16.5	86.9	0.236	0.264	4.62	3.7		1120		-3	22.483

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.41	1.48	58.5		0.78	0.895	1.08

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
ELECTRON CRYSTALLOGRAPHY	MOLECULAR REPLACEMENT	THROUGHOUT	Ideal model	1.41	16.47	1006	112	86.73	0.2396	0.2347	0.2817	RANDOM	18.371

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]
1.08		0.01	-1.13		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	75.764
r_dihedral_angle_3_deg	6.335
r_dihedral_angle_1_deg	5.506
r_mcangle_it	5.296
r_mcbond_it	3.934
r_angle_other_deg	3.442
r_angle_refined_deg	1.977
r_mcbond_other	1.925
r_bond_other_d	0.154
r_chiral_restr	0.065

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	75.764
r_dihedral_angle_3_deg	6.335
r_dihedral_angle_1_deg	5.506
r_mcangle_it	5.296
r_mcbond_it	3.934
r_angle_other_deg	3.442
r_angle_refined_deg	1.977
r_mcbond_other	1.925
r_bond_other_d	0.154
r_chiral_restr	0.065
r_bond_refined_d	0.02
r_gen_planes_refined	0.006
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	66
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Coot	model building

Sample
Human alpha-synuclein

Specimen Preparation
Sample Aggregation State	3D ARRAY

3D Reconstruction
Reconstruction Method	CRYSTALLOGRAPHY

Data Acquisition

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
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.