6V4S | pdb_00006v4s

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VL0	2VL0, 4HFI
experimental model	PDB	4HFI	2VL0, 4HFI

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 (Depositor)	R-Free (Depositor)	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 R01GM157729.