4QCC

Structure of a cube-shaped, highly porous protein cage designed by fusing symmetric oligomeric domains

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	0.1 M MES, pH 6.0, 0.6 M ammonium sulfate, 1% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
6.76	81.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 272.68	α = 90
b = 272.68	β = 90
c = 272.68	γ = 90

Symmetry
Space Group	F 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	100	IMAGE PLATE	RIGAKU RAXIS HTC		2014-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.542

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	7.078	96.407	94.7	0.073	15.62			2526		-3	320.857

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	7.078	7.26	95.1		0.712	1.67

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7.078	96.407	2522	127	94.67	0.2843	0.2826	0.3165	RANDOM	289.798

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
r_dihedral_angle_2_deg	35.751
r_mcangle_it	30.388
r_mcbond_it	17.426
r_mcbond_other	17.424
r_dihedral_angle_3_deg	16.441
r_dihedral_angle_4_deg	9.534
r_dihedral_angle_1_deg	4.927
r_angle_refined_deg	1.183
r_angle_other_deg	0.815
r_chiral_restr	0.065

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.751
r_mcangle_it	30.388
r_mcbond_it	17.426
r_mcbond_other	17.424
r_dihedral_angle_3_deg	16.441
r_dihedral_angle_4_deg	9.534
r_dihedral_angle_1_deg	4.927
r_angle_refined_deg	1.183
r_angle_other_deg	0.815
r_chiral_restr	0.065
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3954
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	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 R01GM133198.