3GD4

Crystal structure of the reduced, NAD-bound form of 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
1VAPOR DIFFUSION, HANGING DROP629810% PEG 4000, 10% isopropanol, 0.1 M Li citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.90734557.693363

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.26α = 90
b = 120.39β = 90
c = 178.19γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray103CCDADSC QUANTUM 315mirrors2002-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.2398ALS5.0.2

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
12.2430.6795.10.0420.036660034570992246.4
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)
2.242.385.30.3330.3673.574.64363

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)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 1GV42.2430.67226004157099303595.110.188610.186840.22209RANDOM46.368
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]
-1.41.350.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.435
r_dihedral_angle_4_deg21.02
r_dihedral_angle_3_deg16.391
r_dihedral_angle_1_deg6.053
r_scangle_it2.551
r_angle_refined_deg1.671
r_scbond_it1.546
r_mcangle_it1.024
r_mcbond_it0.601
r_nbtor_refined0.319
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.435
r_dihedral_angle_4_deg21.02
r_dihedral_angle_3_deg16.391
r_dihedral_angle_1_deg6.053
r_scangle_it2.551
r_angle_refined_deg1.671
r_scbond_it1.546
r_mcangle_it1.024
r_mcbond_it0.601
r_nbtor_refined0.319
r_nbd_refined0.234
r_xyhbond_nbd_refined0.203
r_symmetry_hbond_refined0.164
r_symmetry_vdw_refined0.124
r_chiral_restr0.092
r_bond_refined_d0.012
r_gen_planes_refined0.005
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 Atoms6803
Nucleic Acid Atoms
Solvent Atoms521
Heterogen Atoms194

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling