5KTE | pdb_00005kte

Crystal structure of Deinococcus radiodurans MntH, an Nramp-family transition metal transporter

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4WGW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.5	277	0.1 M sodium acetate pH 4.5, 0.05 M magnesium acetate, 24% PEG400 and 0.4-1 % beta-octylglucoside
2	VAPOR DIFFUSION	4.5	277	0.1 M sodium acetate pH 4.5, 0.05 M magnesium acetate, 24% PEG400 and 0.4-1 % beta-octylglucoside
3	VAPOR DIFFUSION	4.5	277	0.1 M sodium acetate pH 4.5, 0.05 M magnesium acetate, 24% PEG400 and 0.4-1 % beta-octylglucoside

Crystal Properties
Matthews coefficient	Solvent content
4.52	72.78
4.52	72.78
4.52	72.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.131	α = 90
b = 132.077	β = 90
c = 220.995	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	177	CCD	ADSC QUANTUM 315		2011-02-24	M	SINGLE WAVELENGTH
2	2	x-ray	177	CCD	ADSC QUANTUM 315		2011-02-24	M	SINGLE WAVELENGTH
3	3	177	CCD	ADSC QUANTUM 315		2010-08-19

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	1.139	APS	24-ID-C
2	SYNCHROTRON	APS BEAMLINE 24-ID-C	1.139	APS	24-ID-C
3	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.97918	APS	24-ID-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	3.941	46.471	95	0.171	0.99	6	16.6		11791

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	3.94	4.08	96		0.189	0.61	11.4

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4WGW	3.941	46.471	11388	1130	75.98	0.2722	0.2676	0.27	0.3131	0.31

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	8.723
f_angle_d	0.74
f_chiral_restr	0.042
f_plane_restr	0.004
f_bond_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5622
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	3

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing
HKL-2000	data reduction

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.