5HXB

Cereblon in complex with DDB1, CC-885, and GSPT1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4TZ4	4TZ4, 3E1Y
experimental model	PDB	3E1Y	4TZ4, 3E1Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		280	200mM Sodium Citrate, Tris pH 8.5, 18% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.89	68.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 156.747	α = 90
b = 111.522	β = 95.81
c = 175.057	γ = 90

Symmetry
Space Group	P 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r		2015-07-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.0	ALS	5.0.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	3.6	50	94.6	0.198	10.6	4.8		66582

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.6	3.66	93.9		0.796	2.1		3343

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	4TZ4, 3E1Y	3.6	50	62827	3289	94.4	0.226	0.224	0.273	RANDOM	112.3

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]
2.62		1.25	-8.14		5.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.516
r_dihedral_angle_3_deg	24.831
r_dihedral_angle_4_deg	22.38
r_long_range_B_refined	22.277
r_long_range_B_other	22.277
r_mcangle_it	14.634
r_mcangle_other	14.634
r_scangle_other	14.429
r_dihedral_angle_1_deg	12.88
r_mcbond_it	9.514
r_mcbond_other	9.512
r_scbond_it	9.217
r_scbond_other	9.214
r_angle_refined_deg	1.796
r_angle_other_deg	1.012
r_chiral_restr	0.146
r_bond_refined_d	0.017
r_gen_planes_refined	0.017
r_gen_planes_other	0.008
r_bond_other_d	0.004
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	25025
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	64

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing