8BC6

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex an aspartimide degron peptide

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, HANGING DROP		294	0.5 M (NH4)H2PO4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.966	α = 90
b = 59.015	β = 90
c = 88.651	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-F		2018-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.000	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	1.718	37.23	99.6	0.074	1	19.8	12.73		32513

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	1.72	1.82	99.4		1.749	0.632	1.34	12.46

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	FOURIER SYNTHESIS	THROUGHOUT	4V2Y	1.72	37.23	30878	1635	99.83	0.196	0.19459	0.22261	RANDOM	37.924

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]
-0.35			0.93		-0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.504
r_dihedral_angle_3_deg	13.102
r_dihedral_angle_4_deg	9.929
r_dihedral_angle_1_deg	7.351
r_long_range_B_refined	6.625
r_long_range_B_other	6.623
r_scangle_other	3.74
r_mcangle_it	2.485
r_mcangle_other	2.484
r_scbond_it	2.439
r_scbond_other	2.438
r_angle_refined_deg	1.753
r_mcbond_it	1.663
r_mcbond_other	1.662
r_angle_other_deg	1.405
r_chiral_restr	0.094
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2221
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms	44

Software

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