Experiment: 9DKZ

ELECTRON CRYSTALLOGRAPHY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1H8U
in silico model	AlphaFold	AF-P13727-F1-model_v4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.24	α = 90
b = 57.87	β = 90
c = 59.06	γ = 90

Symmetry
Space Group	P 2 21 21

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	3.2		96.1	0.69	0.719	0.931	3.2			1912			85.01

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)
1	3.2	3.29		98	4.13	4.29	0.559

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
ELECTRON CRYSTALLOGRAPHY		FREE R-VALUE	3.2	28.93	1882	199	95.58	0.2727	0.2679	0.2858	0.311	0.3431	Random selection	91.79

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	12.6272
f_angle_d	1.0433
f_chiral_restr	0.0573
f_plane_restr	0.007
f_bond_d	0.0055

Software

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

Sample
In situ microED structure of the Eosinophil major basic protein-1

Specimen Preparation
Sample Aggregation State	CELL
Vitrification Instrument	LEICA EM GP
Cryogen Name	ETHANE
Sample Vitrification Details	Blot time of 6~8 sec, single-side back blotting

3D Reconstruction
Reconstruction Method	CRYSTALLOGRAPHY
Number of Particles
Reported Resolution (Å)	3.2
Resolution Method	DIFFRACTION PATTERN/LAYERLINES
Other Details
Refinement Type
Symmetry Type	3D CRYSTAL
Space Group Name
Length a	31.24
Length b	57.87
Length c	57.87
Angle Alpha	90
Angle Beta	90
Angle Gamma	90

Map-Model Fitting and Refinement
Id	1 (1h8u)
Refinement Space	RECIPROCAL
Refinement Protocol	OTHER
Refinement Target
Overall B Value
Fitting Procedure
Details	Alternating rounds of phenix.refine and map filling in Coot

Data Acquisition
Detector Type	FEI CETA (4k x 4k)
Electron Dose (electrons/Å**2)	0.15

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS 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
IMAGE ACQUISITION	EPU	1.13
MODEL FITTING	Coot	0.9.8.92
MOLECULAR REPLACEMENT	PHENIX	1.21.1-5286
RECONSTRUCTION	PHENIX	1.21.1-5286
MODEL REFINEMENT	PHENIX	1.21.1_5286

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.