Experiment: 5MND

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5G0Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	IN CELL		293	We used Madex HP (Certisusa). Madex HP contains about 1E13 virus occlusion bodies (OB) per liter and the OBs were purified from the aqueous suspension by applying iterative washing and centrifugation cycles. The pellet was then re-suspended in ultra-pure water at pH7. After 3h of incubation at room temperature the supernatant, containing the almost pure OBs, was removed from the pellet and subjected to filtration steps through a sequence of stainless steel filters with decreasing pore sizes (20 um, 10 um, 5 um, 2 um, 0.5 m; all IDEX). To increase the concentration of CpGV to the desired 1E11 particles/ml for injection at LCLS, the suspension was subjected to centrifugation at 21,000 g, the supernatant was removed, and the pellet re-suspended. Size distribution and particle concentration was estimated using a Nanosight LM14 instrument (Malvern).

Crystal Properties
Matthews coefficient	Solvent content
1.6	23.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.4	α = 90
b = 103.4	β = 90
c = 103.4	γ = 90

Symmetry
Space Group	I 2 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293.15	PIXEL	CS-PAD CXI-2		2015-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE CXI	1.5498	SLAC LCLS	CXI

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.55	32.7	99.2	0.99	35.21	1755.5		6052

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.56	2.651	96.96		0.965	8.57	351.9

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
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5G0Z	2.56	32.7	1.385	6052	601	99.2293818659	0.16	0.154	0.207	Rfree from 5G0Z	21.0136272722

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	15.2507022006
f_angle_d	0.542254716655
f_chiral_restr	0.0449375355728
f_plane_restr	0.00292430002288
f_bond_d	0.00270642187068

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2031
Nucleic Acid Atoms
Solvent Atoms	80
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

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.