6R1K | pdb_00006r1k

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 7c


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
1.8232.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.23α = 90
b = 60.08β = 90
c = 88.52γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-04-01MSINGLE 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
11.8547.4699.80.06121.4612.9526327
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)
11.851.9698.91.030.862.2513

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4V2Y1.9447.4621565113599.740.177040.175180.180.212220.22RANDOM46.107
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]
0.361.93-2.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.868
r_dihedral_angle_4_deg19.642
r_dihedral_angle_3_deg14.016
r_long_range_B_refined6.602
r_long_range_B_other6.585
r_dihedral_angle_1_deg6.422
r_scangle_other4.499
r_mcangle_it3.125
r_mcangle_other3.125
r_scbond_it2.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.868
r_dihedral_angle_4_deg19.642
r_dihedral_angle_3_deg14.016
r_long_range_B_refined6.602
r_long_range_B_other6.585
r_dihedral_angle_1_deg6.422
r_scangle_other4.499
r_mcangle_it3.125
r_mcangle_other3.125
r_scbond_it2.9
r_scbond_other2.887
r_mcbond_it2.087
r_mcbond_other2.087
r_angle_refined_deg1.768
r_angle_other_deg1.052
r_chiral_restr0.111
r_bond_refined_d0.016
r_gen_planes_refined0.009
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 Atoms2454
Nucleic Acid Atoms
Solvent Atoms123
Heterogen Atoms84

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling