5MND

SFX structure of Cydia pomonella granulovirus using a double flow-focusing nozzle

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	FREE ELECTRON LASER
Source details	SLAC LCLS BEAMLINE CXI
Synchrotron site	SLAC LCLS
Beamline	CXI
Temperature [K]	293.15
Detector technology	PIXEL
Collection date	2015-06-26
Detector	CS-PAD CXI-2
Wavelength(s)	1.5498
Spacegroup name	I 2 3
Unit cell lengths	103.400, 103.400, 103.400
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	32.700 - 2.560
R-factor	0.16
Rwork	0.154
R-free	0.20700
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	5g0z
RMSD bond length	0.003
RMSD bond angle	0.542
Data reduction software	CrystFEL
Data scaling software	CrystFEL
Phasing software	PHASER
Refinement software	PHENIX (1.11_2567)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	32.700	2.651
High resolution limit [Å]	2.550	2.560
Number of reflections	6052
<I/σ(I)>	35.21	8.57
Completeness [%]	99.2	96.96
Redundancy	1755.5	351.9
CC(1/2)	0.990	0.965

Crystallization Conditions

crystal 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).