6ZEU

Crystal structure of proteinase K lamella by electron diffraction with a 50 micrometre C2 condenser aperture

ELECTRON CRYSTALLOGRAPHY

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.331	α = 90
b = 67.331	β = 90
c = 106.878	γ = 90

Symmetry
Space Group	P 43 21 2

Data Collection

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.06	92.4		1.3	1.45	0.627	0.611	1.8	9.1

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 (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
ELECTRON CRYSTALLOGRAPHY	MOLECULAR REPLACEMENT	FREE R-VALUE	2ID8	2.004	57.034	15759	793	91.825	0.201	0.1991	0.2343	Random selection	16.43

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]
-0.418			-0.418		0.836

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.271
r_dihedral_angle_4_deg	16.718
r_dihedral_angle_3_deg	13.967
r_lrange_it	5.677
r_scangle_it	5.529
r_dihedral_angle_1_deg	5.049
r_scbond_it	4.714
r_mcangle_it	3.124
r_mcbond_it	2.646
r_angle_refined_deg	1.509

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.271
r_dihedral_angle_4_deg	16.718
r_dihedral_angle_3_deg	13.967
r_lrange_it	5.677
r_scangle_it	5.529
r_dihedral_angle_1_deg	5.049
r_scbond_it	4.714
r_mcangle_it	3.124
r_mcbond_it	2.646
r_angle_refined_deg	1.509
r_nbtor_refined	0.316
r_symmetry_xyhbond_nbd_refined	0.277
r_nbd_refined	0.206
r_symmetry_nbd_refined	0.201
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.054
r_bond_refined_d	0.043
r_gen_planes_refined	0.003

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Sample
proteinase K

Specimen Preparation
Sample Aggregation State	3D ARRAY
Vitrification Instrument
Cryogen Name	ETHANE
Sample Vitrification Details	Excess liquid was removed by blotting for 4-6s with a Vitrobot

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	67.3308
Length b	67.3308
Length c	67.3308
Angle Alpha	90
Angle Beta	90
Angle Gamma	90

Map-Model Fitting and Refinement
Id	1 (2ID8)
Refinement Space	RECIPROCAL
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	OTHER	OTHER
Electron Dose (electrons/Å**2)	0.034	0.034

Imaging Experiment	1
Date of Experiment	2018-04-20
Temperature (Kelvin)
Microscope Model	FEI TALOS ARCTICA
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

EM Software
Task	Software Package	Version
MODEL REFINEMENT	REFMAC	5.8.0258
MOLECULAR REPLACEMENT	Phaser	2.8.2
SYMMETRY DETERMINATION	POINTLESS	1.11.12
CRYSTALLOGRAPHY MERGING	AIMLESS	0.7.1

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.