5OH4

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Piperidine-2,6-dione (Glutarimide)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4V2Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	0.1 M sodium acetate pH 4.6, 15 %(W/V) PEG 20000

Crystal Properties
Matthews coefficient	Solvent content
1.8	30

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.18	α = 90
b = 59.661	β = 90
c = 88.289	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2011-09-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.3	37.1	97	0.08	1	8.64	2.55		13628

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)	Redundancy	Number Unique Reflections (All)
1	2.3	2.44	94		0.37	0.86	1.98	2.52

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4V2Y	2.3	37.1	12940	678	98.75	0.19228	0.18929	0.25008	RANDOM	42.714

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]
-0.72			3.54		-2.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.268
r_dihedral_angle_4_deg	16.806
r_dihedral_angle_3_deg	15.125
r_dihedral_angle_1_deg	5.953
r_long_range_B_refined	4.751
r_long_range_B_other	4.74
r_scangle_other	2.788
r_mcangle_it	2.019
r_mcangle_other	2.018
r_scbond_it	1.736
r_scbond_other	1.736
r_angle_refined_deg	1.463
r_angle_other_deg	1.315
r_mcbond_other	1.296
r_mcbond_it	1.295
r_chiral_restr	0.076
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.007
r_gen_planes_other	0.007
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 Atoms	Number
Protein Atoms	2415
Nucleic Acid Atoms
Solvent Atoms	69
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling