8A5N

X-ray structure of human H-chain ferritin treated with SDS


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5N27 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP92932.0 M magnesium chloride 0.1 M bicine buffer pH 9.0
Crystal Properties
Matthews coefficientSolvent content
3.0759.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 183.92α = 90
b = 183.92β = 90
c = 183.92γ = 90
Symmetry
Space GroupF 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2022-06-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 11.2C0.96ELETTRA11.2C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.52106.1899.50.1850.1850.016141.22041266
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.521.551000.8592.415

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5N271.52106.1841266205699.4890.1530.15130.190322.741
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_deg38.741
r_dihedral_angle_4_deg20.723
r_dihedral_angle_3_deg13.037
r_lrange_it8.141
r_lrange_other7.75
r_dihedral_angle_1_deg5.563
r_scangle_it5.448
r_scangle_other5.446
r_scbond_it3.59
r_scbond_other3.588
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.741
r_dihedral_angle_4_deg20.723
r_dihedral_angle_3_deg13.037
r_lrange_it8.141
r_lrange_other7.75
r_dihedral_angle_1_deg5.563
r_scangle_it5.448
r_scangle_other5.446
r_scbond_it3.59
r_scbond_other3.588
r_mcangle_it3.461
r_mcangle_other3.445
r_mcbond_it2.282
r_mcbond_other2.25
r_angle_refined_deg1.815
r_angle_other_deg1.607
r_symmetry_xyhbond_nbd_refined0.47
r_xyhbond_nbd_refined0.269
r_nbd_refined0.254
r_symmetry_xyhbond_nbd_other0.244
r_nbd_other0.183
r_symmetry_nbd_other0.179
r_nbtor_refined0.176
r_symmetry_nbd_refined0.176
r_chiral_restr0.102
r_symmetry_nbtor_other0.086
r_metal_ion_refined0.059
r_symmetry_metal_ion_refined0.015
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1424
Nucleic Acid Atoms
Solvent Atoms355
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing