7JGW

Crystal structure of BCL-XL in complex with COMPOUND 1620116, CRYSTAL FORM 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3INQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M sodium acetate (pH 5.0) 10% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.0439.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.098α = 90
b = 54.665β = 90
c = 113.506γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-10-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.9537Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.335.7198.20.9990.0264.235752
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.330.859

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 REPLACEMENTTHROUGHOUT3INQ1.335.7133781182497.640.16710.16540.1985RANDOM21.667
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]
2.020.4-2.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.166
r_dihedral_angle_4_deg22.283
r_dihedral_angle_3_deg12.158
r_dihedral_angle_1_deg5.658
r_rigid_bond_restr2.4
r_angle_other_deg1.505
r_angle_refined_deg1.453
r_chiral_restr0.08
r_gen_planes_refined0.009
r_bond_refined_d0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.166
r_dihedral_angle_4_deg22.283
r_dihedral_angle_3_deg12.158
r_dihedral_angle_1_deg5.658
r_rigid_bond_restr2.4
r_angle_other_deg1.505
r_angle_refined_deg1.453
r_chiral_restr0.08
r_gen_planes_refined0.009
r_bond_refined_d0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1164
Nucleic Acid Atoms
Solvent Atoms109
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing