6V4S

A Closed pore conformation of a Pentameic ligand-gated ion channel with additional N-terminal domain

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	100 mM Tris pH 7.5, 250 mM CaCl2, 14.5% (w/v) PEG-MME 2000

Crystal Properties
Matthews coefficient	Solvent content
4.5	72.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 159.406	α = 90
b = 337.254	β = 90
c = 111.812	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	193	PIXEL	DECTRIS PILATUS 6M		2016-06-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.9786	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	3.55	48.18	99.6	0.999	11	13.3		73420

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.55	3.64	95.5		0.372		12.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2VL0, 4HFI	3.55	48.04	62330	3250	88.99	0.1972	0.1935	0.2681	RANDOM	140.679

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]
-10.69			18.68		-7.99

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	83.697
r_sphericity_bonded	41.827
r_dihedral_angle_2_deg	38.774
r_dihedral_angle_3_deg	20.95
r_dihedral_angle_4_deg	16.803
r_dihedral_angle_1_deg	8.998
r_angle_refined_deg	2.269
r_rigid_bond_restr	2.033
r_angle_other_deg	1.224
r_chiral_restr	0.138

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	83.697
r_sphericity_bonded	41.827
r_dihedral_angle_2_deg	38.774
r_dihedral_angle_3_deg	20.95
r_dihedral_angle_4_deg	16.803
r_dihedral_angle_1_deg	8.998
r_angle_refined_deg	2.269
r_rigid_bond_restr	2.033
r_angle_other_deg	1.224
r_chiral_restr	0.138
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	22983
Nucleic Acid Atoms
Solvent Atoms	5
Heterogen Atoms	268

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
MOLREP	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 R01GM133198.