6R0U

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 5a and hydrolysis product


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2940.4 M Ammonium phosphate
Crystal Properties
Matthews coefficientSolvent content
1.8433.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.952α = 90
b = 59.583β = 90
c = 89.053γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-04-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.747.98990.0730.99920.2212.3433924
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.898.20.950.8812.75

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 REPLACEMENTTHROUGHOUT4V2Y1.747.9832233168898.960.188920.186940.22674RANDOM36.033
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]
-0.671.94-1.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.59
r_dihedral_angle_4_deg14.713
r_dihedral_angle_3_deg13.839
r_dihedral_angle_1_deg6.658
r_long_range_B_refined6.574
r_long_range_B_other6.543
r_scangle_other3.849
r_mcangle_it3.109
r_mcangle_other3.108
r_scbond_it2.455
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.59
r_dihedral_angle_4_deg14.713
r_dihedral_angle_3_deg13.839
r_dihedral_angle_1_deg6.658
r_long_range_B_refined6.574
r_long_range_B_other6.543
r_scangle_other3.849
r_mcangle_it3.109
r_mcangle_other3.108
r_scbond_it2.455
r_scbond_other2.451
r_mcbond_it2.065
r_mcbond_other2.065
r_angle_refined_deg2.062
r_angle_other_deg1.079
r_chiral_restr0.129
r_bond_refined_d0.019
r_gen_planes_refined0.012
r_bond_other_d0.003
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 Atoms2481
Nucleic Acid Atoms
Solvent Atoms185
Heterogen Atoms78

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling