6QGJ

Structure of human Bcl-2 in complex with fragment/ABT-263 hybrid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6QGG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52840.15M KSCN, 20% PEG1500 and 0.1M Na acetate buffer pH 5.5
Crystal Properties
Matthews coefficientSolvent content
1.9938.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.989α = 90
b = 56.173β = 90
c = 64.417γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2009-06-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

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
11.753099.10.03419.53.916972
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)
11.751.81980.5393.8

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 REPLACEMENTTHROUGHOUT6qgg1.9101258261698.630.2020.20090.2248RANDOM36.654
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]
3.47-1.25-2.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.244
r_dihedral_angle_4_deg15.895
r_dihedral_angle_3_deg14.749
r_dihedral_angle_1_deg5.044
r_angle_refined_deg1.903
r_angle_other_deg1.096
r_chiral_restr0.08
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.244
r_dihedral_angle_4_deg15.895
r_dihedral_angle_3_deg14.749
r_dihedral_angle_1_deg5.044
r_angle_refined_deg1.903
r_angle_other_deg1.096
r_chiral_restr0.08
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1174
Nucleic Acid Atoms
Solvent Atoms83
Heterogen Atoms67

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata reduction
MOLREPphasing