4LTO | pdb_00004lto

Bacterial sodium channel in high calcium, I222 space group

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3RVY	PDB ENTRIES 3RVY, 4DXW, AND 4EKW
experimental model	PDB	4DXW	PDB ENTRIES 3RVY, 4DXW, AND 4EKW
experimental model	PDB	4EKW	PDB ENTRIES 3RVY, 4DXW, AND 4EKW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	277	200 mM calcium chloride, 30% PEG400, 100 mM sodium acetate, pH 5.0, 0.5 M TMAO, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
6.93	82.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 147.669	α = 90
b = 161.679	β = 90
c = 162.234	γ = 90

Symmetry
Space Group	I 2 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	100	CCD	ADSC QUANTUM 315r		2011-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.11587	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	3.46	50	94.2	0.14	8.7	10.5	24208	22804

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.46	3.65	72.3		3.074	0.3	2.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRIES 3RVY, 4DXW, AND 4EKW	3.46	15	22952	21766	1186	89.12	0.22578	0.22356	0.25	0.26803	0.3	RANDOM	173.018

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]
16.08			-4.21		-11.87

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	58.23
r_scbond_it	48.637
r_mcangle_it	45.883
r_dihedral_angle_2_deg	38.048
r_mcbond_it	36.685
r_dihedral_angle_3_deg	24.953
r_dihedral_angle_4_deg	23.851
r_dihedral_angle_1_deg	7.841
r_angle_refined_deg	1.656
r_chiral_restr	0.099
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4084
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms	7

Software

Software
Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling