6QG8

Structure of human Bcl-2 in complex with PUMA BH3 peptide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5284from 0.2M MgCl2, 25% PegMME 2k, 0.1M Na Acetate buffer pH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.0540.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.135α = 90
b = 54.95β = 90
c = 84.725γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.979ESRFID29

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
11.850750.1117.13.513577
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)
11.81.8616.70.5341.9

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 REPLACEMENTTHROUGHOUT2yxj1.9201232164784.420.17130.1690.2163RANDOM29.333
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]
0.07-1.771.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.675
r_dihedral_angle_4_deg18.04
r_dihedral_angle_3_deg16.779
r_dihedral_angle_1_deg5.243
r_angle_refined_deg1.485
r_angle_other_deg1.08
r_chiral_restr0.077
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.675
r_dihedral_angle_4_deg18.04
r_dihedral_angle_3_deg16.779
r_dihedral_angle_1_deg5.243
r_angle_refined_deg1.485
r_angle_other_deg1.08
r_chiral_restr0.077
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1270
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
MOLREPphasing