2IMS

The X-ray Structure of a Bak Homodimer Reveals an Inhibitory Zinc Binding Site


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6298PEG 3350 15-30% and 1-50 mM zinc acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1141.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.527α = 90
b = 53.662β = 115.05
c = 58.281γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X8C1.514NSLSX8C

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
11.4710098.60.040.02936.53.6527012703821
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)
11.471.5286.70.4870.3482.172.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.4852.725678135599.590.18050.179250.20402RANDOM19.219
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]
0.5-0.120.06-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it4.75
r_dihedral_angle_1_deg4.713
r_scbond_it2.968
r_mcangle_it1.804
r_angle_refined_deg1.437
r_mcbond_it0.968
r_angle_other_deg0.847
r_symmetry_vdw_other0.258
r_nbd_other0.244
r_nbd_refined0.233
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it4.75
r_dihedral_angle_1_deg4.713
r_scbond_it2.968
r_mcangle_it1.804
r_angle_refined_deg1.437
r_mcbond_it0.968
r_angle_other_deg0.847
r_symmetry_vdw_other0.258
r_nbd_other0.244
r_nbd_refined0.233
r_symmetry_vdw_refined0.196
r_symmetry_hbond_refined0.189
r_xyhbond_nbd_refined0.186
r_nbtor_other0.084
r_chiral_restr0.078
r_metal_ion_refined0.051
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_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 Atoms1300
Nucleic Acid Atoms
Solvent Atoms152
Heterogen Atoms1

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
SOLVEphasing