8OU6

Cereblon isoform 4 in complex with novel Benzamide-Type Cereblon Binder 11c


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4V2Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2940.5 M (NH4)H2PO4
Crystal Properties
Matthews coefficientSolvent content
1.7931.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.989α = 90
b = 59.126β = 90
c = 87.139γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 S 16M2022-08-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.000SLSX10SA

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
11.8437.121000.99916.6212.926237
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)
11.841.910.618

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.8437.122621313081000.1840.22543.73
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]
0.1050.608-0.713
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.042
r_dihedral_angle_2_deg9.634
r_scangle_it7.601
r_scangle_other7.24
r_dihedral_angle_1_deg6.853
r_mcangle_it5.541
r_mcangle_other5.539
r_scbond_it5.365
r_scbond_other5.01
r_mcbond_it4.108
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.042
r_dihedral_angle_2_deg9.634
r_scangle_it7.601
r_scangle_other7.24
r_dihedral_angle_1_deg6.853
r_mcangle_it5.541
r_mcangle_other5.539
r_scbond_it5.365
r_scbond_other5.01
r_mcbond_it4.108
r_mcbond_other4.105
r_angle_refined_deg1.352
r_angle_other_deg0.542
r_nbd_other0.249
r_nbd_refined0.194
r_nbtor_refined0.191
r_xyhbond_nbd_refined0.172
r_metal_ion_refined0.111
r_chiral_restr0.072
r_gen_planes_refined0.008
r_bond_refined_d0.007
r_bond_other_d0.007
r_gen_planes_other0.001
r_dihedral_angle_4_deg
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1990
Nucleic Acid Atoms
Solvent Atoms55
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing