4FDC

Crystal structure of the E493V mutant of human apoptosis inducing factor (AIF)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1microbatch under oil8.529830% PEG 1500, 0.1 M TrisHCl pH 8.5, 4% acetone, microbatch under oil, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5652.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.4α = 90
b = 62.7β = 118.57
c = 101.922γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray103IMAGE PLATEMAR scanner 345 mm platemirrors2011-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-11.0SSRLBL7-1

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
12.439.594.20.4511.36.8214752000584.9
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)
12.42.46288.70.533.16.83224

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1M6I2.439.52147520005108294.180.255480.25320.29678RANDOM130.215
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]
-0.56-0.080.5-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.723
r_dihedral_angle_3_deg17.126
r_dihedral_angle_4_deg15.941
r_dihedral_angle_1_deg5.858
r_angle_refined_deg1.185
r_chiral_restr0.082
r_bond_refined_d0.007
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3555
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms53

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling