5V3O | pdb_00005v3o

Cereblon in complex with DDB1 and CC-220


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293200mM NaCl, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.564.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.029α = 90
b = 126.886β = 90
c = 172.487γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252015-04-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.9787APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
13.250.011000.08919.85.840911

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT3.250.0138828202399.830.206930.203810.20.267330.26RANDOM95.204
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]
-0.420.090.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.678
r_dihedral_angle_4_deg19.117
r_dihedral_angle_3_deg18.582
r_dihedral_angle_1_deg8.43
r_long_range_B_refined7.571
r_long_range_B_other7.571
r_mcangle_it5.142
r_mcangle_other5.142
r_scangle_other4.632
r_mcbond_it3.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.678
r_dihedral_angle_4_deg19.117
r_dihedral_angle_3_deg18.582
r_dihedral_angle_1_deg8.43
r_long_range_B_refined7.571
r_long_range_B_other7.571
r_mcangle_it5.142
r_mcangle_other5.142
r_scangle_other4.632
r_mcbond_it3.001
r_mcbond_other2.999
r_scbond_other2.667
r_scbond_it2.666
r_angle_other_deg2.068
r_angle_refined_deg1.506
r_chiral_restr0.081
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11141
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing