5MIU

G307E variant of Murine Apoptosis Inducing Factor (oxidized state)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GD3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29330% PEG 4000,0.2 M sodium acetate, pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.7154.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.04α = 90
b = 110.06β = 90
c = 119.59γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2015-12-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97895ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
13.548.799.40.03930.9735.35.416448
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.53.5999.80.12950.7351.85.71197

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 REPLACEMENTTHROUGHOUT3GD33.548.71559085799.380.215240.211750.27857RANDOM72.943
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]
-6.89-3.4810.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.851
r_dihedral_angle_3_deg18.818
r_dihedral_angle_4_deg16.459
r_long_range_B_refined8.844
r_long_range_B_other8.844
r_scangle_other5.835
r_mcangle_it5.39
r_mcangle_other5.39
r_dihedral_angle_1_deg5.376
r_angle_other_deg3.639
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.851
r_dihedral_angle_3_deg18.818
r_dihedral_angle_4_deg16.459
r_long_range_B_refined8.844
r_long_range_B_other8.844
r_scangle_other5.835
r_mcangle_it5.39
r_mcangle_other5.39
r_dihedral_angle_1_deg5.376
r_angle_other_deg3.639
r_scbond_it3.486
r_scbond_other3.485
r_mcbond_it3.213
r_mcbond_other3.212
r_angle_refined_deg1.302
r_chiral_restr0.083
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_gen_planes_other0.003
r_bond_other_d
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 Atoms6955
Nucleic Acid Atoms
Solvent Atoms25
Heterogen Atoms106

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing