6V4A

An open conformation of a Pentameic ligand-gated ion channel with additional N-terminal domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6FLI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2910.3 M NH4-Formate, 0.1 M Tris 7.5, 30% (v/v) PEG-MME 500
Crystal Properties
Matthews coefficientSolvent content
3.9969.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 141.064α = 90
b = 116.028β = 109.17
c = 169.63γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray193PIXELDECTRIS PILATUS 6M2016-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.9786SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
13.8348.6199.30.9997.63.849576
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.833.930.448

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 REPLACEMENTTHROUGHOUT6FLI3.832534738187673.330.25740.25560.2914RANDOM145.969
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]
-3.81-0.444.66-0.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.313
r_dihedral_angle_3_deg19.221
r_dihedral_angle_4_deg12.985
r_dihedral_angle_1_deg7.463
r_angle_refined_deg1.983
r_angle_other_deg1.169
r_chiral_restr0.134
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.313
r_dihedral_angle_3_deg19.221
r_dihedral_angle_4_deg12.985
r_dihedral_angle_1_deg7.463
r_angle_refined_deg1.983
r_angle_other_deg1.169
r_chiral_restr0.134
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms23051
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms142

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing