5CMR

Crystal Structure of Linker-Mediated Zn-bound Human H-Ferritin variant 122H-delta C-star


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529850 mM CHES, 150 mM sodium chloride, 0.3 mM zinc chloride, 1 mM H2BDH
Crystal Properties
Matthews coefficientSolvent content
3.7166.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 155.32α = 90
b = 155.32β = 90
c = 155.32γ = 90
Symmetry
Space GroupI 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-04-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.98SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
13.792109.82899.80.1850.1940.0561211.23401340194.54
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.7941000.5550.5550.162512.1481

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2CEI3.79254.9141.37340034599.560.21240.20740.25681.9409
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
f_dihedral_angle_d17.312
f_angle_d1.067
f_chiral_restr0.046
f_plane_restr0.007
f_bond_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1421
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms27

Software

Software
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
Cootmodel building
SCALAdata scaling
MOSFLMdata reduction
MOLREPphasing