7SWC | pdb_00007swc

MicroED structure of proteinase K from a 550 nm thick lamella measured at 300 kV

ELECTRON CRYSTALLOGRAPHY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6CL7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.51	α = 90
b = 68.51	β = 90
c = 104.86	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1						2020-10-01

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	2.9	20	90	0.436	0.534	0.231	0.773	2.43	2.8		27529			18.26

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)
	2.9	2.98	90.4		0.926	1.133	0.384

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	Mean Isotropic B
ELECTRON CRYSTALLOGRAPHY	MOLECULAR REPLACEMENT	FREE R-VALUE	6CL7	2.9	29.41	1.35	9511	627	90.03	0.241	0.2386	0.2745	4.83

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	4.4645
f_angle_d	0.5833
f_chiral_restr	0.0448
f_plane_restr	0.0044
f_bond_d	0.0042

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2029
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Sample
Proteinase K

Specimen Preparation
Sample Aggregation State	3D ARRAY
Vitrification Instrument	LEICA PLUNGER
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	CRYSTALLOGRAPHY
Number of Particles
Reported Resolution (Å)
Resolution Method	DIFFRACTION PATTERN/LAYERLINES
Other Details
Refinement Type
Symmetry Type	3D CRYSTAL
Space Group Name
Length a	68.51
Length b	68.51
Length c	68.51
Angle Alpha	90
Angle Beta	90
Angle Gamma	90

Map-Model Fitting and Refinement
Id	1 (6CL7)
Refinement Space	RECIPROCAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	Maximum likelihood
Overall B Value	5
Fitting Procedure
Details

Data Acquisition
Detector Type	FEI CETA (4k x 4k)
Electron Dose (electrons/Å**2)	0.01

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	DIFFRACTION
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	Coot
CRYSTALLOGRAPHY MERGING	AIMLESS
RECONSTRUCTION	PHENIX
MODEL REFINEMENT	PHENIX

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
NONE

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.