8OU7

Cereblon isoform 4 in complex with novel Benzamide-Type Cereblon Binder 11d

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		294	0.5 M (NH4)H2PO4

Crystal Properties
Matthews coefficient	Solvent content
1.82	32.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.409	α = 90
b = 59.548	β = 90
c = 88.413	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 EIGER2 S 16M		2022-06-17	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)	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	1.7	47.554	99.98	0.999	14.74	12.85		33503

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.761			0.619

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.7	47.554	33465	1676	99.985	0.179	0.1762	0.2237	37.081

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]
-0.229			0.488		-0.259

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	18.739
r_dihedral_angle_3_deg	13.567
r_dihedral_angle_2_deg	10.029
r_lrange_it	9.901
r_lrange_other	9.9
r_scangle_it	8.346
r_scangle_other	8.344
r_dihedral_angle_1_deg	6.313
r_scbond_it	6.093
r_scbond_other	6.091
r_mcangle_it	5.838
r_mcangle_other	5.836
r_mcbond_other	4.782
r_mcbond_it	4.781
r_angle_refined_deg	1.809
r_angle_other_deg	0.653
r_dihedral_angle_other_2_deg	0.218
r_nbd_other	0.218
r_symmetry_nbd_other	0.211
r_nbtor_refined	0.193
r_nbd_refined	0.192
r_symmetry_nbd_refined	0.152
r_xyhbond_nbd_refined	0.129
r_ncsr_local_group_1	0.124
r_ncsr_local_group_3	0.123
r_ncsr_local_group_2	0.115
r_chiral_restr	0.11
r_metal_ion_refined	0.11
r_symmetry_nbtor_other	0.088
r_symmetry_xyhbond_nbd_refined	0.082
r_bond_refined_d	0.015
r_gen_planes_refined	0.014
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2295
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms	63

Software

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