3E1M

Crystal structure of E. coli Bacterioferritin (BFR) obtained after soaking APO-BFR crystals for 2.5 minutes in FE2+ (2.5M FE(II)-BFR)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP52981.8 M AMMONIUM SULFATE, 0.1 M TRI- SODIUM CITRATE PH 5.0. SUBSEQUENTLY, APO-BFR CRYSTALS WERE SOAKED IN A CRYOPROTECTANCT CONTAINING FE2+ AND BUFFERED USING MOPS PH 7 IN PLACE OF CITRATE PH 5. EXPOSURE TO IRON WAS LIMITED TO 2.5 MINUTES BEFORE FLASH FREEZING IN LIQUID NITROGEN. SEE PAPER FOR FULL DETAILS., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, pH 5.00
Crystal Properties
Matthews coefficientSolvent content
3.4864.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 207.972α = 90
b = 207.972β = 90
c = 142.878γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCD2006-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX10.1SRSPX10.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.73285.30.10114.47.4731811
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.72.8546.80.2254.74.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.732.0469466367885.10.2420.2410.259RANDOM5.87
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]
-0.39-0.390.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.842
r_dihedral_angle_3_deg23.711
r_dihedral_angle_4_deg21.766
r_dihedral_angle_1_deg5.062
r_scangle_it2.845
r_scbond_it1.827
r_angle_refined_deg1.76
r_mcangle_it1.028
r_mcbond_it0.684
r_nbtor_refined0.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.842
r_dihedral_angle_3_deg23.711
r_dihedral_angle_4_deg21.766
r_dihedral_angle_1_deg5.062
r_scangle_it2.845
r_scbond_it1.827
r_angle_refined_deg1.76
r_mcangle_it1.028
r_mcbond_it0.684
r_nbtor_refined0.323
r_symmetry_vdw_refined0.276
r_nbd_refined0.244
r_xyhbond_nbd_refined0.16
r_chiral_restr0.148
r_symmetry_hbond_refined0.126
r_metal_ion_refined0.019
r_bond_refined_d0.017
r_gen_planes_refined0.005
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_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15804
Nucleic Acid Atoms
Solvent Atoms246
Heterogen Atoms374

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling