5A3E | pdb_00005a3e

2.5A structure of lysozyme determined by MicroED with data from a single crystal

ELECTRON CRYSTALLOGRAPHY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3J6K	PDB ENTRY 3J6K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.5		pH 4.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.89	α = 90
b = 75.89	β = 90
c = 36.93	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	electron	100				2014-02-05

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.5	11.2	80.1		3.4		3116

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	2.5	2.6	80.1		0.292		3.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	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-Free (Depositor)	Mean Isotropic B
ELECTRON CRYSTALLOGRAPHY	MOLECULAR REPLACEMENT	PDB ENTRY 3J6K	2.501	11.189	1.46	3115	142	78.35	0.2152	0.2131	0.2531

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	12.347
f_angle_d	0.687
f_chiral_restr	0.03
f_plane_restr	0.004
f_bond_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	992
Nucleic Acid Atoms
Solvent Atoms	10
Heterogen Atoms

Software

Software
Software Name	Purpose
PHASER	model building
PHENIX	refinement
Aimless	data scaling
PHASER	phasing

Sample
Lysozyme

Specimen Preparation
Sample Aggregation State	3D ARRAY

3D Reconstruction
Reconstruction Method	CRYSTALLOGRAPHY
Number of Particles
Reported Resolution (Å)
Resolution Method
Other Details
Refinement Type
Symmetry Type	3D CRYSTAL

Data Acquisition
Detector Type	GENERIC CCD
Electron Dose (electrons/Å**2)

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TECNAI F20
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
Acceleration Voltage (kV)	200
Imaging Details

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.