5AMH

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thalidomide, trigonal crystal form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4V2YPDB ENTRY 4V2Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1100 MM SODIUM ACETATE PH 4.6, 2.2 M CALCIUM CHLORIDE
Crystal Properties
Matthews coefficientSolvent content
2.348

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.72α = 90
b = 51.72β = 90
c = 84.71γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-06-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.230.899.70.0611.853.9141611-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.21.2799.30.741.783.69

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 REPLACEMENTTHROUGHOUTPDB ENTRY 4V2Y1.230.7739531207699.820.127160.125650.15737RANDOM24.966
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]
0.290.150.29-0.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.583
r_sphericity_free30.891
r_sphericity_bonded19.896
r_dihedral_angle_4_deg14.455
r_dihedral_angle_3_deg12.964
r_scbond_it7.159
r_dihedral_angle_1_deg6.723
r_rigid_bond_restr6.304
r_mcangle_it4.943
r_mcbond_it4.802
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.583
r_sphericity_free30.891
r_sphericity_bonded19.896
r_dihedral_angle_4_deg14.455
r_dihedral_angle_3_deg12.964
r_scbond_it7.159
r_dihedral_angle_1_deg6.723
r_rigid_bond_restr6.304
r_mcangle_it4.943
r_mcbond_it4.802
r_mcbond_other4.774
r_angle_refined_deg2.398
r_angle_other_deg1.96
r_chiral_restr0.127
r_bond_refined_d0.023
r_gen_planes_refined0.014
r_gen_planes_other0.01
r_bond_other_d0.001
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms827
Nucleic Acid Atoms
Solvent Atoms149
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing