7NFL | pdb_00007nfl

An octameric barrel state of a de novo coiled-coil assembly: CC-Type2-(LaId)4-I24N.

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	9	292	After 1:1 dilution with the peptide solution, the resulting conditions were 50 mM 2-(bis(2-hydroxyethyl)amino)acetic acid (BICINE) and 5% v/v 2-methyl-2,4-pentanediol (MPD).

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.465	α = 90
b = 47.465	β = 90
c = 127.7	γ = 90

Symmetry
Space Group	I 4 2 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	1.44	44.51	99.7	0.125	0.128	0.026	0.999	14.5	24.1		13654			24.63

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	1.44	1.48	99.1		9.999	14.351	3.129	0.591	0.6	21.1

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	1.44	44.49	12979	671	99.37	0.1807	0.179	0.18	0.2125	0.22	RANDOM	31.791

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]
2.06			2.06		-4.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	47.725
r_dihedral_angle_3_deg	14.021
r_rigid_bond_restr	3.677
r_dihedral_angle_1_deg	3.43
r_angle_other_deg	1.646
r_angle_refined_deg	1.455
r_chiral_restr	0.091
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	47.725
r_dihedral_angle_3_deg	14.021
r_rigid_bond_restr	3.677
r_dihedral_angle_1_deg	3.43
r_angle_other_deg	1.646
r_angle_refined_deg	1.455
r_chiral_restr	0.091
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	444
Nucleic Acid Atoms
Solvent Atoms	38
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.