8OIZ

Crystal structure of human CRBN-DDB1 in complex with Pomalidomide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5V3O 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.22910.8 microliter of CRBN-DDB1 complex at 25 mg/mL (including 1 mM compound and 2 % DMSO final) plus 0.8 microliter of a crystallisation solution consisting of 0.1 M Hepes pH 8.2, 0.2 M NaCl and 10-16 % PEG Smear Medium, plus 0.2 microliter of seeds (established from the same conditions), against 500 microliter of crystallisation solution.
Crystal Properties
Matthews coefficientSolvent content
2.3948.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.841α = 90
b = 128.508β = 90
c = 198.377γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2019-01-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
12.549.591000.2360.2460.0670.9936.713.26447467.44
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)
12.52.5699.83.3033.4370.9470.45713.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.549.596438432871000.21580.21330.2615RANDOM67.13
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]
11.7034-11.1786-0.5248
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion18.16
t_omega_torsion2.92
t_angle_deg0.96
t_bond_d0.007
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion18.16
t_omega_torsion2.92
t_angle_deg0.96
t_bond_d0.007
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11156
Nucleic Acid Atoms
Solvent Atoms491
Heterogen Atoms45

Software

Software
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
DIALSdata reduction