7NFL

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)
TypeSourceAccession CodeDetails
in silico modelOthermodel helices

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9292After 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 coefficientSolvent content
2.7855.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.465α = 90
b = 47.465β = 90
c = 127.7γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-01-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9159DiamondI04-1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.4444.5199.70.1250.1280.0260.99914.524.11365424.63
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)RedundancyNumber Unique Reflections (All)
11.441.4899.19.99914.3513.1290.5910.621.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTmodel helices1.4444.491297967199.370.18070.1790.2125RANDOM31.791
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]
2.062.06-4.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg47.725
r_dihedral_angle_3_deg14.021
r_rigid_bond_restr3.677
r_dihedral_angle_1_deg3.43
r_angle_other_deg1.646
r_angle_refined_deg1.455
r_chiral_restr0.091
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg47.725
r_dihedral_angle_3_deg14.021
r_rigid_bond_restr3.677
r_dihedral_angle_1_deg3.43
r_angle_other_deg1.646
r_angle_refined_deg1.455
r_chiral_restr0.091
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms444
Nucleic Acid Atoms
Solvent Atoms38
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
Aimlessdata scaling
xia2data scaling
PHASERphasing