5OCV

A Rare Lysozyme Crystal Form Solved Using High-Redundancy 3D Electron Diffraction Data from Micron-Sized Needle Shaped Crystals

ELECTRON CRYSTALLOGRAPHY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		3.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.72	α = 90
b = 103.88	β = 90
c = 31.65	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1		97

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	2.2	28.68	79.7		42.4		9516

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.28	64.3			25.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation 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	R-Free	R-Free Selection Details	Mean Isotropic B
ELECTRON CRYSTALLOGRAPHY	MOLECULAR REPLACEMENT	FREE R-VALUE	1AKI	2.2	28.673	1.35	9516	476	79.73	0.2382	0.2365	0.27	Random	34.77

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	18.762
f_angle_d	0.55
f_chiral_restr	0.042
f_plane_restr	0.003
f_bond_d	0.002

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHASER	phasing

Sample
3D crystals of Lysozyme C from Gallus gallus

Specimen Preparation
Sample Aggregation State	3D ARRAY
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	CRYSTALLOGRAPHY
Number of Particles
Reported Resolution (Å)	2.2
Resolution Method	OTHER
Other Details
Refinement Type
Symmetry Type	3D CRYSTAL
Space Group Name
Length a	67.72
Length b	103.88
Length c	103.88
Angle Alpha	90
Angle Beta	90
Angle Gamma	90

Map-Model Fitting and Refinement
Id	1
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	OTHER
Electron Dose (electrons/Å**2)	0.16

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	JEOL 2100
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	DIFFRACTION
Specimen Holder Model	GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER
Nominal Magnification
Calibrated Magnification
Source	LAB6
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.11.1
MODEL REFINEMENT	Coot	0.8.8
MOLECULAR REPLACEMENT	PHASER	2.7.16
CRYSTALLOGRAPHY MERGING	XSCALE	Nov 1, 2016

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 R01GM133198.