8OU3

Cereblon isoform 4 in complex with novel Benzamide-Type Cereblon Binder 8d


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
1.8132.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.793α = 90
b = 59.519β = 90
c = 88.149γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 S 16M2021-08-27MSINGLE 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
11.4749.3399.970.99915.2812.951535
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)
11.471.5230.6641.09

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.4749.32751535257799.9730.2160.21470.237831.333
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]
-0.3540.493-0.139
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg19.404
r_dihedral_angle_3_deg11.461
r_dihedral_angle_2_deg7.227
r_dihedral_angle_1_deg6.619
r_lrange_it6.414
r_scangle_it5.28
r_scbond_it3.462
r_mcangle_it3.089
r_mcbond_it2.072
r_angle_refined_deg1.503
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg19.404
r_dihedral_angle_3_deg11.461
r_dihedral_angle_2_deg7.227
r_dihedral_angle_1_deg6.619
r_lrange_it6.414
r_scangle_it5.28
r_scbond_it3.462
r_mcangle_it3.089
r_mcbond_it2.072
r_angle_refined_deg1.503
r_nbtor_refined0.319
r_symmetry_nbd_refined0.3
r_nbd_refined0.202
r_xyhbond_nbd_refined0.188
r_metal_ion_refined0.114
r_symmetry_xyhbond_nbd_refined0.103
r_chiral_restr0.082
r_gen_planes_refined0.012
r_bond_refined_d0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2254
Nucleic Acid Atoms
Solvent Atoms110
Heterogen Atoms75

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing