8OU4 | pdb_00008ou4

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

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
1.8	31.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.511	α = 90
b = 59.542	β = 90
c = 88.185	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	2.25	47.58	99.84	0.998	10.68	12.9		14648

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	2.25	2.331			0.631

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	2.25	47.58	14646	731	99.857	0.224	0.2218	0.22	0.2685	0.26	53.339

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]
-0.241			0.147		0.094

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.06
r_dihedral_angle_3_deg	10.903
r_dihedral_angle_2_deg	6.687
r_dihedral_angle_1_deg	6.003
r_lrange_it	3.768
r_lrange_other	3.767
r_scangle_it	2.297
r_scangle_other	2.296
r_mcangle_it	1.826
r_mcangle_other	1.826
r_scbond_it	1.379
r_scbond_other	1.379
r_mcbond_it	1.068
r_mcbond_other	1.068
r_angle_refined_deg	0.758
r_angle_other_deg	0.309
r_nbd_other	0.221
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.179
r_metal_ion_refined	0.175
r_symmetry_xyhbond_nbd_refined	0.165
r_nbd_refined	0.159
r_symmetry_nbd_refined	0.146
r_xyhbond_nbd_refined	0.12
r_symmetry_nbtor_other	0.082
r_ncsr_local_group_1	0.078
r_ncsr_local_group_3	0.074
r_ncsr_local_group_2	0.067
r_chiral_restr	0.038
r_dihedral_angle_other_2_deg	0.028
r_symmetry_xyhbond_nbd_other	0.01
r_bond_other_d	0.004
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2185
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms	41

Software

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