8CPC

3D electron diffraction structure of Hen Egg-White Lysozyme from nano-crystals obtained by high pressure freezing and cryo-sectioning

ELECTRON CRYSTALLOGRAPHY

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Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.887	α = 90
b = 76.887	β = 90
c = 37.761	γ = 90

Symmetry
Space Group	P 43 21 2

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 (All)	R-Work	R-Free	Mean Isotropic B
ELECTRON CRYSTALLOGRAPHY		FREE R-VALUE	2.91	54.367	2638	276	96.418	0.214	0.2048	0.2949	31.961

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]
-0.063			-0.063		0.125

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.428
r_dihedral_angle_3_deg	21.077
r_dihedral_angle_4_deg	17.784
r_dihedral_angle_1_deg	8.368
r_lrange_it	6.524
r_lrange_other	6.521
r_mcangle_other	3.819
r_mcangle_it	3.797
r_scangle_it	3.41
r_scangle_other	3.409
r_mcbond_it	2.165
r_mcbond_other	2.102
r_scbond_it	1.897
r_scbond_other	1.875
r_angle_refined_deg	1.489
r_angle_other_deg	1.205
r_nbd_refined	0.225
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.169
r_nbd_other	0.16
r_xyhbond_nbd_refined	0.158
r_symmetry_nbd_refined	0.117
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.059
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Software

Software
Software Name	Purpose
REFMAC	refinement

Sample
Monomer of Hen Egg-White Lysozyme

Specimen Preparation
Sample Aggregation State	3D ARRAY
Vitrification Instrument
Cryogen Name	NITROGEN
Sample Vitrification Details	Freezing carried out at high pressure (210 MPa) and -196 C, using a Leica EM HPM100
Staining Type	NONE
Staining Material	Brilliant blue
Staining Details	The blue dye (Brillant blue) is used to see the crystals during cryo-sectioning
Embedding Material	dextran
Embedding Details	40% Dextran in phosphate buffer

3D Reconstruction
Reconstruction Method	CRYSTALLOGRAPHY
Number of Particles
Reported Resolution (Å)	2.91
Resolution Method	DIFFRACTION PATTERN/LAYERLINES
Other Details	Diffraction data were processed with XDS and merged with XSCALE. The structure was solved by molecular replacement with PHASER 2.8.3 and refined with Refmac 5.8.0267, using electron atomic scattering factors (source electron used in Refmac).
Refinement Type
Symmetry Type	3D CRYSTAL
Space Group Name
Length a	76.89
Length b	76.89
Length c	76.89
Angle Alpha	90
Angle Beta	90
Angle Gamma	90

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

Data Acquisition
Detector Type	OTHER
Electron Dose (electrons/Å**2)	0.004

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	GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details	Camera length used 730 mm and 1000 mm (corresponding to 1285 and 1825 mm calibrated values)

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
NONE