5MIV

G307E variant of murine Apoptosis Inducing Factor in complex with NAD+


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GD4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29310% PEG 6000, 0.1 M HEPES, pH 7.0, 1 mM NADH
Crystal Properties
Matthews coefficientSolvent content
3.6866.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.43α = 90
b = 116.78β = 90
c = 166.48γ = 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)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
13.143.599.50.9926.64.526576
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)
13.13.180.3311.34.71946

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 REPLACEMENTTHROUGHOUT3GD43.143.525254132299.520.201210.197950.26269RANDOM95.513
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]
6.990.69-7.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.658
r_dihedral_angle_4_deg19.007
r_dihedral_angle_3_deg17.994
r_long_range_B_refined13.578
r_long_range_B_other13.564
r_mcangle_other8.941
r_mcangle_it8.94
r_scangle_other8.741
r_dihedral_angle_1_deg6.336
r_mcbond_it5.649
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.658
r_dihedral_angle_4_deg19.007
r_dihedral_angle_3_deg17.994
r_long_range_B_refined13.578
r_long_range_B_other13.564
r_mcangle_other8.941
r_mcangle_it8.94
r_scangle_other8.741
r_dihedral_angle_1_deg6.336
r_mcbond_it5.649
r_mcbond_other5.644
r_scbond_it5.277
r_scbond_other5.27
r_angle_other_deg3.576
r_angle_refined_deg1.536
r_chiral_restr0.077
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_gen_planes_other0.004
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 Atoms6833
Nucleic Acid Atoms
Solvent Atoms125
Heterogen Atoms194

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing