2JD7

Crystal Structure of the Fe-soaked Ferritin from the Hyperthermophilic Archaeal Anaerobe Pyrococcus furiosus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2JD6REFINED 2JD6 COORDINATES

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1THE CRYSTALS USED FOR DATA COLLECTION WERE GROWN AGAINST 0.5 ML OF 2 M AMMONIUM SULPHATE RESERVOIR SOLUTION, WITH DROPS CONTAINING 2 MICRO-L OF 5 MG/ML PROTEIN SOLUTION IN 50 MM HEPES, PH 7 AND EQUAL AMOUNT OF THE RESERVOIR SOLUTION. IRON SOAKING OF FERRITIN CRYSTALS WAS PERFORMED BY TRANSFERRING THEM TO A 10-20 MICRO-L DROP OF A SOLUTION WITH COMPOSITION 20 MM FESO4, 2 MM NA2S2O4, 25 % GLYCEROL AND 2 M AMMONIUM SULFATE, FOR 15 MINUTES.
Crystal Properties
Matthews coefficientSolvent content
469

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 254.301α = 90
b = 342.878β = 90
c = 266.221γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRSEARCHCOLLIMATING AND FOCUSSING MIRRO2006-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
12.84299.10.088.23.628040760.5
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)
12.82.9594.10.3522.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Free (Depositor)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTREFINED 2JD6 COORDINATES2.8204.122661731418799.10.2010.1990.25RANDOM39.42
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]
1.52-1.4-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.271
r_dihedral_angle_3_deg19.208
r_dihedral_angle_4_deg17.239
r_scangle_it7.241
r_dihedral_angle_1_deg5.469
r_scbond_it4.847
r_mcangle_it3.374
r_mcbond_it2.084
r_angle_refined_deg1.467
r_nbtor_refined0.32
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49788
Nucleic Acid Atoms
Solvent Atoms368
Heterogen Atoms238

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling