5YIZ

Mouse Cereblon thalidomide binding domain complexed with racemic thalidomide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3WX2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2771.0M ammonium sulfate 0.1M sodium acetate (pH5.0)
Crystal Properties
Matthews coefficientSolvent content
2.4449.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 201.376α = 90
b = 201.376β = 90
c = 123.358γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2011-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0000SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
125010020.65.8125695

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 REPLACEMENTTHROUGHOUT3WX2238.06119353631199.90.185410.183980.21252RANDOM29.197
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.925
r_dihedral_angle_4_deg25.533
r_dihedral_angle_3_deg16.086
r_dihedral_angle_1_deg7.893
r_long_range_B_refined7.714
r_long_range_B_other7.528
r_scangle_other5.65
r_scbond_it4.208
r_scbond_other4.178
r_mcangle_other3.757
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.925
r_dihedral_angle_4_deg25.533
r_dihedral_angle_3_deg16.086
r_dihedral_angle_1_deg7.893
r_long_range_B_refined7.714
r_long_range_B_other7.528
r_scangle_other5.65
r_scbond_it4.208
r_scbond_other4.178
r_mcangle_other3.757
r_mcangle_it3.752
r_angle_other_deg3.493
r_mcbond_other2.62
r_mcbond_it2.619
r_angle_refined_deg0.961
r_chiral_restr0.076
r_gen_planes_other0.037
r_gen_planes_refined0.018
r_bond_refined_d0.005
r_bond_other_d
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 Atoms11838
Nucleic Acid Atoms
Solvent Atoms980
Heterogen Atoms470

Software

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