5XHM

Crystal structure of Frog M-ferritin D40A mutant


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP92772.0 M MgCl2 and 100 mM Bicine (pH 9.0)
Crystal Properties
Matthews coefficientSolvent content
3.3263.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 184.17α = 90
b = 184.17β = 90
c = 184.17γ = 90
Symmetry
Space GroupF 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray103IMAGE PLATERIGAKU RAXIS IV++2016-01-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
11.723.9810030.71329984
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.731006.311.7

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 REPLACEMENTTHROUGHOUT3KA31.723.9828484146199.890.157790.156310.18735RANDOM16.428
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_deg38.31
r_dihedral_angle_4_deg15.018
r_dihedral_angle_3_deg14.792
r_long_range_B_refined6.17
r_long_range_B_other6.021
r_dihedral_angle_1_deg5.271
r_scangle_other4.818
r_scbond_it3.578
r_scbond_other3.576
r_mcangle_other1.843
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.31
r_dihedral_angle_4_deg15.018
r_dihedral_angle_3_deg14.792
r_long_range_B_refined6.17
r_long_range_B_other6.021
r_dihedral_angle_1_deg5.271
r_scangle_other4.818
r_scbond_it3.578
r_scbond_other3.576
r_mcangle_other1.843
r_mcangle_it1.842
r_mcbond_it1.318
r_mcbond_other1.309
r_angle_refined_deg1.105
r_angle_other_deg0.687
r_chiral_restr0.067
r_gen_planes_refined0.017
r_bond_refined_d0.009
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms1430
Nucleic Acid Atoms
Solvent Atoms264
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing