4ITV

Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains, triple mutant, P212121 form

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BRO	1BRO and 1AA7
experimental model	PDB	1AA7	1BRO and 1AA7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.4	298	0.1M Na Citrate pH 4.4, 10% PEG 3000, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.62	α = 90
b = 156.61	β = 90
c = 321.15	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	PSI PILATUS 6M		2012-10-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97910	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	3.598	160.575	98.3	0.066	16.61		76475	76475		-3	102.21

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	3.6	3.69	95.7		0.619	2.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	1BRO and 1AA7	3.598	96.14	1.99	76445	76445	3821	98.28	0.2078	0.2078	0.2061	0.2402	random	151.8637

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	13.192
f_angle_d	0.609
f_chiral_restr	0.042
f_plane_restr	0.004
f_bond_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	40776
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

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.