6ZET | pdb_00006zet

Crystal structure of proteinase K nanocrystals by electron diffraction with a 20 micrometre C2 condenser aperture

ELECTRON CRYSTALLOGRAPHY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ID8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.365	α = 90
b = 67.365	β = 90
c = 106.784	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)
	2.7	2.83	83.6		1.275	1.389	0.533	0.498	1.8	10.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
ELECTRON CRYSTALLOGRAPHY	MOLECULAR REPLACEMENT	FREE R-VALUE	2ID8	2.701	57.04	6184	297	85.925	0.227	0.2247	0.236	0.2679	0.2816	7.281

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]
-0.134			-0.134		0.267

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.442
r_dihedral_angle_4_deg	19.975
r_dihedral_angle_3_deg	16.12
r_scangle_it	5.536
r_lrange_it	5.499
r_dihedral_angle_1_deg	5.026
r_scbond_it	4.897
r_mcangle_it	3.796
r_mcbond_it	2.992
r_angle_refined_deg	1.207
r_nbtor_refined	0.315
r_symmetry_xyhbond_nbd_refined	0.216
r_nbd_refined	0.203
r_symmetry_nbd_refined	0.191
r_xyhbond_nbd_refined	0.143
r_chiral_restr	0.053
r_metal_ion_refined	0.036
r_bond_refined_d	0.007
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	67.3653
Length b	67.3653
Length c	67.3653
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	OTHER	OTHER	OTHER	OTHER	OTHER	OTHER
Electron Dose (electrons/Å**2)	0.034	0.034	0.034	0.034	0.034	0.034	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
MOLECULAR REPLACEMENT	Phaser	2.8.2
SYMMETRY DETERMINATION	POINTLESS	1.11.12
CRYSTALLOGRAPHY MERGING	AIMLESS	0.7.1
MODEL REFINEMENT	REFMAC	5.8.0258

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details