7NFJ | pdb_00007nfj

A heptameric barrel state of a de novo coiled-coil assembly: CC-Type2-(LaId)4-L28Y.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		model helices

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	292	After 1:1 dilution with the peptide solution, the resulting conditions were 50 mM sodium 2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonate (sodium HEPES), 5% w/v PEG 8000 and 4% v/v ethylene glycol.

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.539	α = 90
b = 130.416	β = 90
c = 38.454	γ = 90

Symmetry
Space Group	P 21 21 2

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	DECTRIS PILATUS 6M-F		2018-01-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9159	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.19	45.58	98.5	0.043	0.046	0.013	0.997	18	10.7		78107			17.62

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.19	1.22	91.2		0.893	0.982	0.397	0.723	1.6	5.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	model helices	1.19	45.53	71552	3764	94.82	0.1692	0.1675	0.17	0.2039	0.21	RANDOM	28.718

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]
1.17			-1.86		0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.445
r_dihedral_angle_3_deg	14.212
r_rigid_bond_restr	5.975
r_dihedral_angle_1_deg	3.612
r_angle_refined_deg	1.847
r_angle_other_deg	1.675
r_chiral_restr	0.126
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.445
r_dihedral_angle_3_deg	14.212
r_rigid_bond_restr	5.975
r_dihedral_angle_1_deg	3.612
r_angle_refined_deg	1.847
r_angle_other_deg	1.675
r_chiral_restr	0.126
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1614
Nucleic Acid Atoms
Solvent Atoms	110
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
Aimless	data scaling
xia2	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.