9GV1 | pdb_00009gv1

NavMs F208L bound to sevoflurane

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6SX5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	30.8% PEG300 100mM HEPES 100mM NaCl

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.703	α = 90
b = 108.703	β = 90
c = 209.157	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	80	PIXEL	DECTRIS EIGER X 16M	Toroidal mirror	2023-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97626	ESRF	ID23-1

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	2.2	48.2	100	1	28.6	20		32204

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	2.2	9	100		0.973	4.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.2	48.2	32202	1656	99.953	0.223	0.2214	0.2221	0.252	0.2515	66.684

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]
2.31			2.31		-4.619

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.432
r_lrange_it	13.968
r_dihedral_angle_6_deg	13.437
r_scangle_it	12.664
r_mcangle_it	10.296
r_scbond_it	9.274
r_mcbond_it	7.807
r_dihedral_angle_1_deg	5.873
r_dihedral_angle_2_deg	5.635
r_angle_refined_deg	2.127

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.432
r_lrange_it	13.968
r_dihedral_angle_6_deg	13.437
r_scangle_it	12.664
r_mcangle_it	10.296
r_scbond_it	9.274
r_mcbond_it	7.807
r_dihedral_angle_1_deg	5.873
r_dihedral_angle_2_deg	5.635
r_angle_refined_deg	2.127
r_nbtor_refined	0.32
r_nbd_refined	0.236
r_symmetry_nbd_refined	0.184
r_xyhbond_nbd_refined	0.153
r_chiral_restr	0.143
r_symmetry_xyhbond_nbd_refined	0.127
r_bond_refined_d	0.013
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1966
Nucleic Acid Atoms
Solvent Atoms	51
Heterogen Atoms	92

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	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.