1NF6

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)
TypeSourceAccession CodeDetails
experimental modelOtheras-isolated model for this protein; phases obtained by MAD at the iron K edge.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5293ammonium sulfate, sodium acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2954

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 225.79α = 90
b = 225.79β = 90
c = 225.79γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4toroidal mirrors2001-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.353096.50.0626.83.115233615233635
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.352.43990.2162.73.115292

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONstructure solved using the native as-isolated structure as starting modelTHROUGHOUTas-isolated model for this protein; phases obtained by MAD at the iron K edge.2.3530149010149010304396.50.1970.1970.267thin resolution shells28
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 MethodRefinement High ResolutionRefinement Low Resolution
23645.6
RMS Deviations
KeyRefinement Restraint Deviation
s_non_zero_chiral_vol0.022
s_from_restr_planes0.016
s_angle_d0.015
s_bond_d0.004
s_anti_bump_dis_restr
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms21134
Nucleic Acid Atoms
Solvent Atoms1811
Heterogen Atoms584

Software

Software
Software NamePurpose
SHELXL-97refinement
SCALAdata scaling
CNSrefinement
DENZOdata reduction
CCP4data scaling
CNSphasing