8RDT | pdb_00008rdt

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with spiro-isoxazol based compound 8j


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3 mM Thalidomide
Crystal Properties
Matthews coefficientSolvent content
1.831.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.441α = 90
b = 59.488β = 90
c = 88.11γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 S 16M2023-04-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.0000SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
11.9549.30399.90.1060.99910.677.014176845.965
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.0799.61.8170.5241.057.19

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1.9549.321143111199.790.200880.198780.210.241690.25RANDOM44.494
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]
-0.891.29-0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.846
r_dihedral_angle_4_deg13.669
r_dihedral_angle_3_deg12.624
r_dihedral_angle_1_deg7.112
r_long_range_B_refined4.874
r_long_range_B_other4.872
r_scangle_other3.358
r_mcangle_it2.361
r_mcangle_other2.361
r_scbond_it2.184
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.846
r_dihedral_angle_4_deg13.669
r_dihedral_angle_3_deg12.624
r_dihedral_angle_1_deg7.112
r_long_range_B_refined4.874
r_long_range_B_other4.872
r_scangle_other3.358
r_mcangle_it2.361
r_mcangle_other2.361
r_scbond_it2.184
r_scbond_other2.126
r_angle_refined_deg1.624
r_mcbond_it1.599
r_mcbond_other1.597
r_angle_other_deg1.347
r_chiral_restr0.068
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms2275
Nucleic Acid Atoms
Solvent Atoms56
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Cootmodel building