9FYH | pdb_00009fyh

Dye Type Peroxidase Aa from Streptomyces lividans by microcrystal electron diffraction (MicroED/3D ED)

ELECTRON CRYSTALLOGRAPHY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6I43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.77	α = 90
b = 67.4	β = 105.8
c = 73.63	γ = 90

Symmetry
Space Group	P 1 21 1

Data Collection

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	MOLECULAR REPLACEMENT	FREE R-VALUE	2.4	19.46	1.34	46115	2962	87.76	0.2053	0.2019	0.2242	0.2561	0.2735	Random selection	18.52

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	9.3745
f_angle_d	0.5571
f_chiral_restr	0.0388
f_plane_restr	0.0049
f_bond_d	0.0025

Sample
Dye type peroxidase Aa

Specimen Preparation
Sample Aggregation State	3D ARRAY
Vitrification Instrument
Cryogen Name	ETHANE
Sample Vitrification Details	Manual blotting in room temperature with ambient humidity

3D Reconstruction
Reconstruction Method	CRYSTALLOGRAPHY
Number of Particles
Reported Resolution (Å)	2.4
Resolution Method	DIFFRACTION PATTERN/LAYERLINES
Other Details
Refinement Type
Symmetry Type	3D CRYSTAL
Space Group Name
Length a	72.77
Length b	67.4
Length c	67.4
Angle Alpha	90
Angle Beta	105.8
Angle Gamma	90

Map-Model Fitting and Refinement
Id	1 (6I43)
Refinement Space	RECIPROCAL
Refinement Protocol	OTHER
Refinement Target	Maximum-likelihood
Overall B Value	18.52
Fitting Procedure
Details

Data Acquisition
Detector Type	FEI CETA (4k x 4k)
Electron Dose (electrons/Å**2)	0.115

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
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 FITTING	PHENIX
MOLECULAR REPLACEMENT	PHENIX
CRYSTALLOGRAPHY MERGING	PHENIX
RECONSTRUCTION	PHENIX
MODEL REFINEMENT	PHENIX

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.