6D91 | pdb_00006d91

Crystal structure of the Deinococcus radiodurans Nramp/MntH divalent transition metal transporter in the outward-open, apo conformation

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6BU5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	6	298	50 mM succinic acid, 20 mM spermidine, 100 mM MES, 26% PEG400

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.919	α = 90
b = 75.508	β = 98.07
c = 53.151	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2017-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.9792	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.356	38.14	63.94	0.1847	0.2026	0.07994	0.986	8.83	4.4		10998			37.61

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.36	2.44	15.6		0.3829	0.5194	0.3478	0.683	1.45	1.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	FREE R-VALUE	6BU5	2.356	38.136	1.35	10604	1061	63.99	0.2492	0.2438	0.24	0.2989	0.3	Random Selection of 5%

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	17.549
f_angle_d	0.524
f_chiral_restr	0.036
f_plane_restr	0.003
f_bond_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3012
Nucleic Acid Atoms
Solvent Atoms	17
Heterogen Atoms	86

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	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.