5FS8

Crystal structure of the G308E mutant of human apoptosis inducing factor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1M6IPDB ENTRY 1M6I

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.2 M AMMONIUM ACETATE AND 20% POLY-ETHYLENE GLYCOL, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.4549.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.79α = 90
b = 89.75β = 94.93
c = 60.33γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARMOSAIC 325 mm CCDMIRRORS2012-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-2SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.437.1797.10.069.43.61024522
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4888.70.621.52.9

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1M6I1.489.7597342507596.810.165830.164430.19247RANDOM23.382
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]
1.09-0.410.55-1.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.201
r_dihedral_angle_4_deg19.351
r_dihedral_angle_3_deg12.343
r_dihedral_angle_1_deg5.829
r_scangle_it2.663
r_mcangle_it1.997
r_scbond_it1.641
r_angle_refined_deg1.541
r_mcbond_it1.216
r_mcbond_other1.216
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.201
r_dihedral_angle_4_deg19.351
r_dihedral_angle_3_deg12.343
r_dihedral_angle_1_deg5.829
r_scangle_it2.663
r_mcangle_it1.997
r_scbond_it1.641
r_angle_refined_deg1.541
r_mcbond_it1.216
r_mcbond_other1.216
r_angle_other_deg0.783
r_chiral_restr0.088
r_bond_refined_d0.011
r_gen_planes_refined0.008
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3665
Nucleic Acid Atoms
Solvent Atoms644
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing