8BB4

Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with C3 linker


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7Q2J 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.829321-28% PEG 3350 0.4 M KSCN 0.1 M HEPES pH 6.8
Crystal Properties
Matthews coefficientSolvent content
2.6353.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.786α = 90
b = 184.506β = 102.78
c = 47.951γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2022-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA0.999998SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.8184.511000.1050.1490.1050.9846219494
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.951000.4590.650.4590.7072

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 REPLACEMENTTHROUGHOUT7Q2J2.892.251857188899.990.20620.20270.279RANDOM48.286
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]
2.812.42-2.27-1.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.4
r_dihedral_angle_1_deg8.311
r_dihedral_angle_2_deg6.423
r_angle_refined_deg1.199
r_angle_other_deg0.433
r_chiral_restr0.052
r_gen_planes_refined0.006
r_bond_refined_d0.005
r_bond_other_d0.004
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4948
Nucleic Acid Atoms
Solvent Atoms58
Heterogen Atoms71

Software

Software
Software NamePurpose
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction