6R19 | pdb_00006r19

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 20a


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
1.7830.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.557α = 90
b = 59.234β = 90
c = 88.425γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-02-14MSINGLE 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
11.4549.2699.80.095114.8312.7553406
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)
11.451.5498.50.890.862.1112.9

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 REPLACEMENTTHROUGHOUT4V2Y1.4549.2650733267399.710.173160.171720.180.200680.21RANDOM23.837
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]
-1.261.20.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.797
r_dihedral_angle_4_deg14.699
r_dihedral_angle_3_deg11.46
r_dihedral_angle_1_deg7.11
r_long_range_B_refined6.101
r_long_range_B_other6.1
r_scangle_other3.178
r_mcangle_other2.327
r_mcangle_it2.325
r_angle_refined_deg2.081
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.797
r_dihedral_angle_4_deg14.699
r_dihedral_angle_3_deg11.46
r_dihedral_angle_1_deg7.11
r_long_range_B_refined6.101
r_long_range_B_other6.1
r_scangle_other3.178
r_mcangle_other2.327
r_mcangle_it2.325
r_angle_refined_deg2.081
r_scbond_it2.076
r_scbond_other2.075
r_mcbond_it1.456
r_mcbond_other1.441
r_angle_other_deg1.066
r_chiral_restr0.119
r_bond_refined_d0.019
r_gen_planes_refined0.012
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 Atoms2564
Nucleic Acid Atoms
Solvent Atoms282
Heterogen Atoms73

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling