6ZHC

PROTAC6 mediated complex of VHL:EloB:EloC and Bcl-xL


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LM81LM8,1MAZ
experimental modelPDB 1MAZ1LM8,1MAZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.52910.2 M Potassium iodide, 0.1 M MES pH 6.5, 23% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.9558.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.99α = 90
b = 101.18β = 90
c = 106.93γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-11.03320CLSI08ID-1

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
11.9247.2799.90.07915.16.559379
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)
11.921.9799.60.6382.55.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1LM8,1MAZ1.9247.2759378291099.8020.1710.16940.195733.4
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]
0.019-0.0390.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.718
r_dihedral_angle_4_deg19.674
r_dihedral_angle_3_deg12.858
r_lrange_it7.329
r_lrange_other7.17
r_dihedral_angle_1_deg6.418
r_scangle_it5.205
r_scangle_other5.204
r_mcangle_it3.637
r_mcangle_other3.636
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.718
r_dihedral_angle_4_deg19.674
r_dihedral_angle_3_deg12.858
r_lrange_it7.329
r_lrange_other7.17
r_dihedral_angle_1_deg6.418
r_scangle_it5.205
r_scangle_other5.204
r_mcangle_it3.637
r_mcangle_other3.636
r_scbond_it3.296
r_scbond_other3.295
r_mcbond_it2.41
r_mcbond_other2.406
r_angle_refined_deg1.252
r_angle_other_deg1.19
r_symmetry_xyhbond_nbd_other0.313
r_symmetry_nbd_refined0.219
r_nbd_other0.212
r_nbd_refined0.194
r_symmetry_nbd_other0.175
r_xyhbond_nbd_refined0.165
r_nbtor_refined0.161
r_symmetry_xyhbond_nbd_refined0.151
r_symmetry_nbtor_other0.085
r_chiral_restr0.055
r_gen_planes_refined0.005
r_bond_refined_d0.004
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3957
Nucleic Acid Atoms
Solvent Atoms460
Heterogen Atoms227

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling