2YXJ

Crystal structure of Bcl-xL in complex with ABT-737


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82980.85M Sodium Citrate, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.551.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.321α = 90
b = 75.37β = 90
c = 87.778γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVAXCO2006-07-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
12.25097.90.10615.053.522532
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)
12.22.281000.3974.23.52262

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 1PQ12.221.9421328115297.730.201280.198720.24931RANDOM38.433
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]
-1.241.040.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.762
r_dihedral_angle_4_deg22.102
r_dihedral_angle_3_deg17.329
r_dihedral_angle_1_deg5.772
r_scangle_it2.528
r_scbond_it1.694
r_angle_refined_deg1.505
r_mcangle_it1.136
r_mcbond_it0.936
r_angle_other_deg0.847
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.762
r_dihedral_angle_4_deg22.102
r_dihedral_angle_3_deg17.329
r_dihedral_angle_1_deg5.772
r_scangle_it2.528
r_scbond_it1.694
r_angle_refined_deg1.505
r_mcangle_it1.136
r_mcbond_it0.936
r_angle_other_deg0.847
r_symmetry_vdw_other0.261
r_nbd_refined0.215
r_nbtor_refined0.198
r_xyhbond_nbd_refined0.19
r_nbd_other0.182
r_symmetry_hbond_refined0.174
r_mcbond_other0.153
r_symmetry_vdw_refined0.134
r_nbtor_other0.092
r_chiral_restr0.079
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2267
Nucleic Acid Atoms
Solvent Atoms201
Heterogen Atoms119

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing