1NF6 | pdb_00001nf6

X-ray structure of the Desulfovibrio desulfuricans bacterioferritin: the diiron site in different catalytic states ("cycled" structure: reduced in solution and allowed to reoxidise before crystallisation)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		as-isolated model for this protein; phases obtained by MAD at the iron K edge.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	ammonium sulfate, sodium acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.29	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 225.79	α = 90
b = 225.79	β = 90
c = 225.79	γ = 90

Symmetry
Space Group	P 21 3

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 4	toroidal mirrors	2001-02-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

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	2.35	30	96.5	0.062	6.8	3.1	152336	152336			35

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	2.35	2.43	99		0.216	2.7	3.1	15292

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	structure solved using the native as-isolated structure as starting model	THROUGHOUT	as-isolated model for this protein; phases obtained by MAD at the iron K edge.	2.35	30	149010	149010	3043	96.5	0.197	0.197	0.189	0.267	0.2493	thin resolution shells	28

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
		23645.6

RMS Deviations
Key	Refinement Restraint Deviation
s_non_zero_chiral_vol	0.022
s_from_restr_planes	0.016
s_angle_d	0.015
s_bond_d	0.004
s_anti_bump_dis_restr

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21134
Nucleic Acid Atoms
Solvent Atoms	1811
Heterogen Atoms	584

Software

Software
Software Name	Purpose
SHELXL-97	refinement
SCALA	data scaling
CNS	refinement
DENZO	data reduction
CCP4	data scaling
CNS	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.