7RVK | pdb_00007rvk

Segment from Y169G mutant of the human prion protein 169-175 GSNQNNF

ELECTRON CRYSTALLOGRAPHY

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	10% w/v PEG8000, 0.1 M MES, pH 6, 0.2 M sodium acetate

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 4.86	α = 90
b = 14.11	β = 93.71
c = 18.41	γ = 101.21

Symmetry
Space Group	P 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 TEMCAM-F416		2016-09-22	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)	CC (Half)	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	13.84	80.3	0.238	0.257	0.98	5.05	6.217		2076			3.58

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1	1.03	64.7		0.43	0.485	0.862	2.25	4.26

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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
ELECTRON CRYSTALLOGRAPHY	AB INITIO PHASING	THROUGHOUT	1	13.84	2075	208	80.3	0.2024	0.1984	0.2501	0.2382	0.2775	RANDOM	5.74

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]
-0.0165	0.1179	0.2173	0.2353	-0.1016	-0.2188

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	24.6
t_omega_torsion	3.14
t_angle_deg	0.94
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	55
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms	8

Software

Software
Software Name	Purpose
XSCALE	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing

Sample
Major prion protein

Specimen Preparation
Sample Aggregation State	3D ARRAY

3D Reconstruction
Reconstruction Method	CRYSTALLOGRAPHY
Number of Particles
Reported Resolution (Å)	1
Resolution Method	DIFFRACTION PATTERN/LAYERLINES
Other Details
Refinement Type
Symmetry Type	3D CRYSTAL
Space Group Name
Length a	4.86
Length b	14.11
Length c	14.11
Angle Alpha	101.21
Angle Beta	93.71
Angle Gamma	101.21

Data Acquisition
Detector Type	TVIPS TEMCAM-F416 (4k x 4k)
Electron Dose (electrons/Å**2)

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TECNAI F30
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)	300
Imaging Details