3E1J

Crystal structure of E. coli Bacterioferritin (BFR) with an unoccupied ferroxidase centre (APO-BFR).


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BCFPDB ENTRY 1BCF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP52891.8 M AMMONIUM SULFATE, 0.1 M TRI- SODIUM CITRATE PH 5.0. CRYSTALS LATER SOAKED IN CRYOPROTECTANT AT PH 7, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K, pH 5.00
Crystal Properties
Matthews coefficientSolvent content
3.4764.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 208.216α = 90
b = 208.216β = 90
c = 142.457γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002006-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
12.73598.80.10114.56.5848971
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)
2.72.8593.70.20251.7

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 1BCF2.735.1180604423998.70.2430.2420.263RANDOM6.29
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]
0.10.1-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.763
r_dihedral_angle_4_deg22.581
r_dihedral_angle_3_deg22.104
r_dihedral_angle_1_deg4.689
r_scangle_it3.354
r_scbond_it2.07
r_angle_refined_deg1.817
r_mcangle_it1.138
r_mcbond_it0.757
r_nbtor_refined0.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.763
r_dihedral_angle_4_deg22.581
r_dihedral_angle_3_deg22.104
r_dihedral_angle_1_deg4.689
r_scangle_it3.354
r_scbond_it2.07
r_angle_refined_deg1.817
r_mcangle_it1.138
r_mcbond_it0.757
r_nbtor_refined0.316
r_symmetry_hbond_refined0.227
r_symmetry_vdw_refined0.226
r_nbd_refined0.225
r_chiral_restr0.17
r_xyhbond_nbd_refined0.159
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_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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15912
Nucleic Acid Atoms
Solvent Atoms399
Heterogen Atoms338

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling