7NFG | pdb_00007nfg

A hexameric barrel state of a de novo coiled-coil assembly: CC-Type2-(LaId)4-L14A.

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, HANGING DROP	6.5	292	After 1:1 dilution with the peptide solution, the resulting conditions were 50 mM sodium cacodylate, 20% 2-methyl-2,4-pentanediol (MPD) and 2.5% PEG 8000.

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.67	α = 90
b = 57.24	β = 90
c = 91.77	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	DECTRIS PILATUS 2M		2015-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9282	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	1.09	14.42	99.9	0.07	0.073	0.021	0.999	13.8	11.8		70145			13.25

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	1.09	1.11	98.8		1.43	1.502	0.454	0.321	1.7	10.6

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	1.09	14.42	66546	3530	99.4	0.1427	0.1414	0.16	0.1695	0.18	RANDOM	19.848

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]
-0.42			-1.73		2.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.433
r_rigid_bond_restr	21.372
r_dihedral_angle_3_deg	11.658
r_dihedral_angle_1_deg	3.342
r_angle_refined_deg	2.18
r_angle_other_deg	1.641
r_chiral_restr	0.111
r_bond_refined_d	0.022
r_gen_planes_refined	0.011
r_bond_other_d	0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.433
r_rigid_bond_restr	21.372
r_dihedral_angle_3_deg	11.658
r_dihedral_angle_1_deg	3.342
r_angle_refined_deg	2.18
r_angle_other_deg	1.641
r_chiral_restr	0.111
r_bond_refined_d	0.022
r_gen_planes_refined	0.011
r_bond_other_d	0.008
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1349
Nucleic Acid Atoms
Solvent Atoms	172
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
Aimless	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.