7SKX

Ab initio structure of proteinase K from electron-counted MicroED data

ELECTRON CRYSTALLOGRAPHY

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Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.08	α = 90
b = 67.08	β = 90
c = 106.78	γ = 90

Symmetry
Space Group	P 43 21 2

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 (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
ELECTRON CRYSTALLOGRAPHY		FREE R-VALUE	1.5	43.386	39303	2001	98.848	0.152	0.1495	0.2046	Random	14.137

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]
-0.47			-0.47		0.939

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.941
r_dihedral_angle_4_deg	21.837
r_dihedral_angle_3_deg	12.286
r_dihedral_angle_1_deg	6.758
r_lrange_it	5.137
r_lrange_other	4.919
r_scangle_it	4.493
r_scangle_other	4.491
r_scbond_it	3.624
r_scbond_other	3.589
r_rigid_bond_restr	2.679
r_mcangle_it	2.35
r_mcangle_other	2.35
r_mcbond_it	1.877
r_mcbond_other	1.858
r_angle_other_deg	1.721
r_angle_refined_deg	1.691
r_symmetry_xyhbond_nbd_refined	0.405
r_symmetry_nbd_refined	0.333
r_nbd_other	0.239
r_nbd_refined	0.221
r_symmetry_nbd_other	0.202
r_nbtor_refined	0.187
r_xyhbond_nbd_refined	0.179
r_xyhbond_nbd_other	0.127
r_symmetry_xyhbond_nbd_other	0.098
r_symmetry_nbtor_other	0.09
r_chiral_restr	0.083
r_metal_ion_refined	0.039
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2029
Nucleic Acid Atoms
Solvent Atoms	234
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement

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	67.08
Length b	67.08
Length c	67.08
Angle Alpha	90
Angle Beta	90
Angle Gamma	90

Map-Model Fitting and Refinement
Id	1
Refinement Space	RECIPROCAL
Refinement Protocol	AB INITIO MODEL
Refinement Target	Maximum likelihood
Overall B Value	14.137
Fitting Procedure
Details

Data Acquisition
Detector Type	FEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)	0.001

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 REFINEMENT	REFMAC
CRYSTALLOGRAPHY MERGING	AIMLESS
RECONSTRUCTION	REFMAC

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