6QGG

Structure of human Bcl-2 in complex with analogue of ABT-737


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YXJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.62841.4M Na/K phosphate pH 5.6
Crystal Properties
Matthews coefficientSolvent content
2.1943.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.277α = 90
b = 55.277β = 90
c = 58.593γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-08-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97DiamondI03

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
11.495094.70.05914.34.127361
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)
11.491.5494.90.1963.8

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 REPLACEMENTTHROUGHOUT2yxj1.51525595121794.630.1520.1510.1732RANDOM16.778
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]
-0.44-0.440.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.522
r_dihedral_angle_4_deg21.754
r_dihedral_angle_3_deg12.554
r_dihedral_angle_1_deg5.207
r_angle_refined_deg1.908
r_angle_other_deg1.189
r_chiral_restr0.111
r_bond_refined_d0.019
r_gen_planes_refined0.012
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.522
r_dihedral_angle_4_deg21.754
r_dihedral_angle_3_deg12.554
r_dihedral_angle_1_deg5.207
r_angle_refined_deg1.908
r_angle_other_deg1.189
r_chiral_restr0.111
r_bond_refined_d0.019
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1137
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms60

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
MOLREPphasing