9ODS | pdb_00009ods

Structure of CRBN TBD bound to compound C3

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7BQU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION		291	0.2M tri-Sodium citrate 18 % w/v PEG 3,350

Crystal Properties
Matthews coefficient	Solvent content
3.36	63.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.559	α = 90
b = 86.279	β = 114.42
c = 90.972	γ = 90

Symmetry
Space Group	C 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	PIXEL	DECTRIS EIGER X 16M		2022-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL10U2	0.97918	SSRF	BL10U2

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	2.61	60.36	62.6	0.99	7	4.1		12509

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	2.61	2.85			0.293

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.61	60.36	11895	614	62.52	0.21642	0.21484	0.2174	0.24802	0.2472	RANDOM	65.14

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]
1.22		0.28	-0.91		-0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.696
r_dihedral_angle_2_deg	11.962
r_dihedral_angle_1_deg	7.24
r_long_range_B_refined	5.067
r_long_range_B_other	5.066
r_mcangle_it	3.015
r_mcangle_other	3.015
r_scangle_other	2.511
r_mcbond_it	1.658
r_mcbond_other	1.658
r_scbond_it	1.351
r_scbond_other	1.351
r_angle_refined_deg	1.02
r_angle_other_deg	0.336
r_chiral_restr	0.047
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3393
Nucleic Acid Atoms
Solvent Atoms	31
Heterogen Atoms	104

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data scaling
XDS	data reduction
PDB_EXTRACT	data extraction
FFT	phasing