3E1Q

Crystal structure of W133F variant E. coli Bacterioferritn with iron.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.8298BFR PROTEIN WAS PRE-LOADED WITH IRON AND THEN CRYSTALLIZED OVERNIGHT IN 1.8 M AMMONIUM SULFATE, 0.1 M MES PH 5.8. PLEASE SEE THE ORIGINAL PAPER FOR FULL DETAILS., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, pH 5.80
Crystal Properties
Matthews coefficientSolvent content
3.4764.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 207.659α = 90
b = 207.659β = 90
c = 142.767γ = 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
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
12.59533.3297.20.1219.313.593115
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)
2.6840.3833.96.9

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 REPLACEMENTTHROUGHOUT2QPI2.633.3188403464997.20.2460.2450.263COPIED AND EXTENDED FROM 2QPI9.85
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]
-0.03-0.030.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.881
r_dihedral_angle_4_deg22.806
r_dihedral_angle_3_deg21.318
r_dihedral_angle_1_deg4.597
r_scangle_it3.5
r_scbond_it2.197
r_angle_refined_deg1.572
r_mcangle_it1.342
r_mcbond_it0.864
r_nbtor_refined0.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.881
r_dihedral_angle_4_deg22.806
r_dihedral_angle_3_deg21.318
r_dihedral_angle_1_deg4.597
r_scangle_it3.5
r_scbond_it2.197
r_angle_refined_deg1.572
r_mcangle_it1.342
r_mcbond_it0.864
r_nbtor_refined0.316
r_symmetry_vdw_refined0.228
r_nbd_refined0.22
r_symmetry_hbond_refined0.168
r_xyhbond_nbd_refined0.16
r_chiral_restr0.131
r_bond_refined_d0.015
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 Atoms15984
Nucleic Acid Atoms
Solvent Atoms433
Heterogen Atoms362

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling