3GD3

Crystal structure of a naturally folded murine apoptosis inducing factor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GV4PDB entry 1GV4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1microbatch under oil729815% PEG 4000, 0.35M KNO3, pH 7.0, microbatch under oil, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6954.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.05α = 90
b = 80.29β = 90
c = 419.64γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray103IMAGE PLATEMAR scanner 345 mm platemirrors2008-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-21.1SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.8408.2581.120.1740.1744.97610804954822
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.82.87369.450.7150.7151.75.06

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 REPLACEMENTTHROUGHOUTPDB entry 1GV42.9546.647134343694210383.420.250950.248610.29965RANDOM95.017
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]
-6.06-0.656.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.123
r_dihedral_angle_3_deg20.869
r_dihedral_angle_4_deg20.288
r_dihedral_angle_1_deg6.98
r_scangle_it3.162
r_scbond_it1.932
r_angle_refined_deg1.77
r_mcangle_it1.559
r_mcbond_it0.991
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.123
r_dihedral_angle_3_deg20.869
r_dihedral_angle_4_deg20.288
r_dihedral_angle_1_deg6.98
r_scangle_it3.162
r_scbond_it1.932
r_angle_refined_deg1.77
r_mcangle_it1.559
r_mcbond_it0.991
r_nbtor_refined0.308
r_nbd_refined0.223
r_symmetry_vdw_refined0.173
r_xyhbond_nbd_refined0.16
r_symmetry_hbond_refined0.127
r_chiral_restr0.103
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14482
Nucleic Acid Atoms
Solvent Atoms27
Heterogen Atoms212

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling