6MSX

Iron containing ferritin at 1.43A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IER 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.4293A 20 uL pellet of 50 mM cadmium sulfate in 2% agar was deposited on a cover slip. Adjacent to this was positioned ferritin (10 ul of 50 mg/ml ferritin, Sigma F4503) and precipitant (10 ul of 3.5M Ammonium Sulfate and 100 mM Tris pH 7.4). The cover slip was equilibrated over 3.5 M Ammonium Sulfate
Crystal Properties
Matthews coefficientSolvent content
3.2161.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 181.59α = 90
b = 181.59β = 90
c = 181.59γ = 90
Symmetry
Space GroupF 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2018-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 17-ID-10.9202NSLS-II17-ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.435099.1431.81138.245041
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.431.4710048.9

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 REPLACEMENTTHROUGHOUT1IER1.435045041229199.140.157920.157160.1717RANDOM30.055
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.427
r_dihedral_angle_4_deg21.854
r_dihedral_angle_3_deg13.755
r_long_range_B_refined8.691
r_long_range_B_other8.11
r_scangle_other7.913
r_scbond_it4.851
r_scbond_other4.85
r_dihedral_angle_1_deg4.46
r_mcangle_other3.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.427
r_dihedral_angle_4_deg21.854
r_dihedral_angle_3_deg13.755
r_long_range_B_refined8.691
r_long_range_B_other8.11
r_scangle_other7.913
r_scbond_it4.851
r_scbond_other4.85
r_dihedral_angle_1_deg4.46
r_mcangle_other3.004
r_mcangle_it2.997
r_angle_refined_deg2.646
r_mcbond_it2.403
r_mcbond_other2.376
r_angle_other_deg1.911
r_chiral_restr0.153
r_bond_refined_d0.03
r_gen_planes_refined0.012
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1365
Nucleic Acid Atoms
Solvent Atoms251
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing