3E1O

Crystal structure of E. coli Bacterioferritin (BFR) with two ZN(II) ION sites at the Ferroxidase centre (ZN-BFR).


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QP7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5298APO-BFR CRYSTALIZED IN 1.8 M AMMONIUM SULFATE, 0.1 M TRI-SODIUM CITRATE PH 5.0. CRYSTAL WAS THEN SOAKED IN A CRYOPROTECTANT CONTAINING ZN2+ IONS AND BUFFERED WITH MOPS PH 7 INSTEAD OF CITRATE. PLEASE SEE PAPER FO FULL DETAILS., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, pH 5.00
Crystal Properties
Matthews coefficientSolvent content
3.4664.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 207.867α = 90
b = 207.867β = 90
c = 142.432γ = 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
12.954589.20.08120.99.1587781
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)
2.953.1189.20.1687.96.5

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 REPLACEMENTTHROUGHOUT2QP72.9544.81557802964890.230.2290.252COPIED AND EXTENDED FROM 2QP7.7.37
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]
0.370.37-0.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.961
r_dihedral_angle_4_deg23.014
r_dihedral_angle_3_deg22.371
r_dihedral_angle_1_deg4.879
r_scangle_it3.482
r_scbond_it2.13
r_angle_refined_deg1.941
r_mcangle_it1.181
r_mcbond_it0.704
r_nbtor_refined0.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.961
r_dihedral_angle_4_deg23.014
r_dihedral_angle_3_deg22.371
r_dihedral_angle_1_deg4.879
r_scangle_it3.482
r_scbond_it2.13
r_angle_refined_deg1.941
r_mcangle_it1.181
r_mcbond_it0.704
r_nbtor_refined0.323
r_symmetry_hbond_refined0.264
r_symmetry_vdw_refined0.249
r_nbd_refined0.24
r_metal_ion_refined0.18
r_chiral_restr0.162
r_xyhbond_nbd_refined0.157
r_bond_refined_d0.022
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_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 Atoms15636
Nucleic Acid Atoms
Solvent Atoms214
Heterogen Atoms362

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling