3E1L

Crystal structure of E. coli Bacterioferritin (BFR) soaked in phosphate with an alternative conformation of the unoccupied Ferroxidase centre (APO-BFR II).


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP52981.8 M AMMOMIUM SULFATE, 0.1 M TRI- SODIUM CITRATE PH 5.0. SUBSEQUENTLY, THE CRYSTALS WERE SOAKED IN A CRYO-PROTECTANT BUFFER CONTAINING PHOSPHATE BUFFERED WITH MOPS PH 7 INSTEAD OF CITRATE. SEE PAPER FOR FULL DETAILS., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, pH 5.00
Crystal Properties
Matthews coefficientSolvent content
3.4964.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 208.082α = 90
b = 208.082β = 90
c = 143.107γ = 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
12.534.296.40.10119.613.91042751
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)
2.52.6480.70.2515.25.7

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 REPLACEMENTTHROUGHOUT2QP72.53499059515796.20.2360.2360.248EXTENDED FROM THE VALIDATION SET USED IN 2QP7.11.67
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]
-0.02-0.020.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.119
r_dihedral_angle_4_deg24.406
r_dihedral_angle_3_deg20.307
r_dihedral_angle_1_deg4.248
r_scangle_it3.493
r_scbond_it2.237
r_angle_refined_deg1.368
r_mcangle_it1.122
r_mcbond_it0.728
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.119
r_dihedral_angle_4_deg24.406
r_dihedral_angle_3_deg20.307
r_dihedral_angle_1_deg4.248
r_scangle_it3.493
r_scbond_it2.237
r_angle_refined_deg1.368
r_mcangle_it1.122
r_mcbond_it0.728
r_nbtor_refined0.307
r_symmetry_vdw_refined0.224
r_nbd_refined0.213
r_symmetry_hbond_refined0.17
r_xyhbond_nbd_refined0.165
r_chiral_restr0.123
r_bond_refined_d0.012
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 Atoms15876
Nucleic Acid Atoms
Solvent Atoms496
Heterogen Atoms337

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling