Experiment: 6HU5

ELECTRON CRYSTALLOGRAPHY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1B2K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				1.5 M SODIUM CHLORIDE

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.849	α = 90
b = 54.38	β = 98.82
c = 71.788	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	electron	100	OTHER	ASI		2018-10-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	LaB6 THERMOIONIC SOURCE

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.8	42.67	66.5	0.655	1.6	2.8		3906

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.97	67.1		0.839	0.8	2.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
ELECTRON CRYSTALLOGRAPHY		NONE	2.8	42.67	1.34	3840	177	63.05	0.2995	0.2975	0.3065	0.339	0.3225	RANDOM

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	13.18
f_angle_d	0.776
f_chiral_restr	0.047
f_bond_d	0.004
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1980
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	3

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
XDS	phasing
CCP4	phasing
PHENIX	refinement

Sample
HWEL

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

3D Reconstruction
Reconstruction Method	CRYSTALLOGRAPHY
Number of Particles
Reported Resolution (Å)	2.8
Resolution Method	DIFFRACTION PATTERN/LAYERLINES
Other Details
Refinement Type
Symmetry Type	3D CRYSTAL
Space Group Name
Length a	31.849
Length b	54.38
Length c	54.38
Angle Alpha	90
Angle Beta	98.82
Angle Gamma	90

Map-Model Fitting and Refinement
Id	1 (1B2K)
Refinement Space
Refinement Protocol	OTHER
Refinement Target	CORRELATION COEF
Overall B Value	10.8
Fitting Procedure
Details

Data Acquisition
Detector Type	OTHER
Electron Dose (electrons/Å**2)	9

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	ZEISS LIBRA120PLUS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	DARK FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	LAB6
Acceleration Voltage (kV)	120
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	PHENIX	1.13
MOLECULAR REPLACEMENT	PHENIX	1.13
MODEL REFINEMENT	PHENIX	1.13

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.