9ODR | pdb_00009odr

Structure of CRBN TBD bound to compound C1

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		277	0.2M tri-Sodium citrate 18 % w/v PEG 3,350

Crystal Properties
Matthews coefficient	Solvent content
3.29	62.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.35	α = 90
b = 87.61	β = 113.98
c = 89.5	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		2023-03-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95373	Australian Synchrotron	MX2

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	2.42	46.84	89.9	0.999	16.2	6.9		20893

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	2.42	2.5			0.681

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	2.42	43.84	20893	1098	89.9	0.18506	0.18261	0.1884	0.22761	0.2346	RANDOM	56.179

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]
-0.17		0.13	0.1		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.805
r_long_range_B_other	11.646
r_long_range_B_refined	11.645
r_scangle_other	9.022
r_dihedral_angle_1_deg	7.911
r_mcangle_it	7.425
r_mcangle_other	7.423
r_dihedral_angle_2_deg	7.141
r_scbond_it	6.155
r_scbond_other	6.153
r_mcbond_it	5.154
r_mcbond_other	5.154
r_angle_refined_deg	1.718
r_angle_other_deg	0.595
r_chiral_restr	0.088
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3383
Nucleic Acid Atoms
Solvent Atoms	46
Heterogen Atoms	108

Software

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