7JGV

CRYSTAL STRUCTURE OF BCL-XL IN COMPLEX WITH COMPOUND 1620116, CRYSTAL FORM 2


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 MME 2000 10% ethanol
Crystal Properties
Matthews coefficientSolvent content
1.8634

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.324α = 90
b = 56.256β = 90
c = 117.756γ = 90
Symmetry
Space GroupP 21 21 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
12.0538.1899.70.99514.4617473
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)
12.052.110.888

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 REPLACEMENTTHROUGHOUT3INQ2.0538.181640789198.850.19210.18920.2459RANDOM28.305
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]
1.17-1.190.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.212
r_dihedral_angle_4_deg13.89
r_dihedral_angle_3_deg13.882
r_dihedral_angle_1_deg5.452
r_angle_refined_deg1.358
r_angle_other_deg1.334
r_chiral_restr0.068
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.212
r_dihedral_angle_4_deg13.89
r_dihedral_angle_3_deg13.882
r_dihedral_angle_1_deg5.452
r_angle_refined_deg1.358
r_angle_other_deg1.334
r_chiral_restr0.068
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2259
Nucleic Acid Atoms
Solvent Atoms160
Heterogen Atoms90

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction