8OU3 | pdb_00008ou3

Cereblon isoform 4 in complex with novel Benzamide-Type Cereblon Binder 8d

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
1.81	32.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.793	α = 90
b = 59.519	β = 90
c = 88.149	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		2021-08-27	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	1.47	49.33	99.97	0.999	15.28	12.9		51535

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	1.47	1.523			0.664	1.09

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.47	49.327	51535	2577	99.973	0.216	0.2147	0.21	0.2378	0.24	31.333

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]
-0.354			0.493		-0.139

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	19.404
r_dihedral_angle_3_deg	11.461
r_dihedral_angle_2_deg	7.227
r_dihedral_angle_1_deg	6.619
r_lrange_it	6.414
r_scangle_it	5.28
r_scbond_it	3.462
r_mcangle_it	3.089
r_mcbond_it	2.072
r_angle_refined_deg	1.503
r_nbtor_refined	0.319
r_symmetry_nbd_refined	0.3
r_nbd_refined	0.202
r_xyhbond_nbd_refined	0.188
r_metal_ion_refined	0.114
r_symmetry_xyhbond_nbd_refined	0.103
r_chiral_restr	0.082
r_gen_planes_refined	0.012
r_bond_refined_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2254
Nucleic Acid Atoms
Solvent Atoms	110
Heterogen Atoms	75

Software

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