7Q2J

Quaternary Complex of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC Homer


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2H9M 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.829321% PEG 3350 0.4 M KSCN 0.1 M HEPES 6.8
Crystal Properties
Matthews coefficientSolvent content
2.5251.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.702α = 90
b = 190.809β = 115.25
c = 48.698γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.999998SLSX06SA

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
12.547.7599.30.9978.87.126976
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)
12.52.60.786

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 REPLACEMENTTHROUGHOUT2H9M2.547.7525571136899.30.24590.24340.2932RANDOM67.574
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]
-6.830.99-9.0710.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.543
r_dihedral_angle_4_deg23.442
r_dihedral_angle_3_deg19.629
r_dihedral_angle_1_deg7.522
r_angle_refined_deg1.429
r_angle_other_deg1.183
r_chiral_restr0.054
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.543
r_dihedral_angle_4_deg23.442
r_dihedral_angle_3_deg19.629
r_dihedral_angle_1_deg7.522
r_angle_refined_deg1.429
r_angle_other_deg1.183
r_chiral_restr0.054
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4932
Nucleic Acid Atoms
Solvent Atoms24
Heterogen Atoms72

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction