2JD6

Crystal Structure of the as isolated Ferritin from the Hyperthermophilic Archaeal Anaerobe Pyrococcus furiosus


X-RAY DIFFRACTION

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.
Crystal Properties
Matthews coefficientSolvent content
469.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 254.097α = 90
b = 341.422β = 90
c = 265.524γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-06-24MSINGLE 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
12.7558.299.70.0816.55.7295335
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)
12.752.997.80.33.13.6

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1VLG2.75204.122803751491499.60.1980.1950.247RANDOM33.98
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]
1.91-0.92-0.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.842
r_dihedral_angle_3_deg18.611
r_dihedral_angle_4_deg15.328
r_scangle_it7.098
r_dihedral_angle_1_deg5.337
r_scbond_it4.778
r_mcangle_it3.252
r_mcbond_it2.074
r_angle_refined_deg1.432
r_nbtor_refined0.321
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.842
r_dihedral_angle_3_deg18.611
r_dihedral_angle_4_deg15.328
r_scangle_it7.098
r_dihedral_angle_1_deg5.337
r_scbond_it4.778
r_mcangle_it3.252
r_mcbond_it2.074
r_angle_refined_deg1.432
r_nbtor_refined0.321
r_nbd_refined0.23
r_symmetry_vdw_refined0.208
r_symmetry_hbond_refined0.186
r_xyhbond_nbd_refined0.13
r_chiral_restr0.099
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49788
Nucleic Acid Atoms
Solvent Atoms790
Heterogen Atoms236

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing