2Y3Q | pdb_00002y3q

1.55A structure of apo bacterioferritin from E. coli


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VXIPDB ENTRY 2VXI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.51.8M AMMONIUM SULPHATE, 100MM ACETATE, PH 5.5
Crystal Properties
Matthews coefficientSolvent content
3.4764.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 208α = 90
b = 208β = 90
c = 142.6γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.5543.298.40.112.84.14384270.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.6199.20.6234.1

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2VXI1.5543.23416504219221000.166520.164760.170.200070.2RANDOM9.22
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_deg40.814
r_dihedral_angle_4_deg22.73
r_dihedral_angle_3_deg11.533
r_sphericity_free6.715
r_angle_other_deg5.565
r_dihedral_angle_1_deg4.807
r_scangle_it4.272
r_scbond_it3.01
r_sphericity_bonded2.251
r_mcangle_it1.728
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15460
Nucleic Acid Atoms
Solvent Atoms2978
Heterogen Atoms691

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing