6R1D | pdb_00006r1d

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 7d, co-crystallized


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29415 % PEG 6K, 5 % Glycerol
Crystal Properties
Matthews coefficientSolvent content
1.7931.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.643α = 90
b = 52.482β = 95.79
c = 59.242γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-05-22MSINGLE 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
11.139.299.10.053117.676.377977
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)
11.11.1695.10.40.923.645.3

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 REPLACEMENTTHROUGHOUT4v2y1.139.2740533898990.123480.122110.120.149630.15RANDOM17.049
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]
0.151.7-0.23-0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free46.684
r_dihedral_angle_2_deg31.055
r_sphericity_bonded21.719
r_scangle_other18.744
r_scbond_it16.057
r_scbond_other16.049
r_dihedral_angle_4_deg14.431
r_long_range_B_refined12.742
r_dihedral_angle_3_deg11.32
r_long_range_B_other11.26
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free46.684
r_dihedral_angle_2_deg31.055
r_sphericity_bonded21.719
r_scangle_other18.744
r_scbond_it16.057
r_scbond_other16.049
r_dihedral_angle_4_deg14.431
r_long_range_B_refined12.742
r_dihedral_angle_3_deg11.32
r_long_range_B_other11.26
r_rigid_bond_restr8.179
r_dihedral_angle_1_deg6.23
r_angle_refined_deg2.449
r_angle_other_deg1.973
r_mcangle_it1.89
r_mcangle_other1.889
r_mcbond_it1.771
r_mcbond_other1.77
r_chiral_restr0.455
r_bond_refined_d0.031
r_gen_planes_refined0.016
r_bond_other_d0.015
r_gen_planes_other0.015
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1663
Nucleic Acid Atoms
Solvent Atoms276
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing