8OIZ

Crystal structure of human CRBN-DDB1 in complex with Pomalidomide

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	DIAMOND BEAMLINE I04
Synchrotron site	Diamond
Beamline	I04
Temperature [K]	100
Detector technology	PIXEL
Collection date	2019-01-27
Detector	DECTRIS EIGER2 XE 16M
Wavelength(s)	0.9795
Spacegroup name	P 21 21 21
Unit cell lengths	71.841, 128.508, 198.377
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	49.590 - 2.500
R-factor	0.2158
Rwork	0.213
R-free	0.26150
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.007
RMSD bond angle	0.960
Data reduction software	DIALS
Data scaling software	Aimless (0.7.3)
Phasing software	PHASER
Refinement software	BUSTER (2.10.4 (17-FEB-2023))

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	49.590	49.590	2.560
High resolution limit [Å]	2.500	11.460	2.500
Rmerge	0.236	0.079	3.303
Rmeas	0.246	0.083	3.437
Rpim	0.067	0.025	0.947
Total number of observations	851075	8201	58886
Number of reflections	64474	778	4509
<I/σ(I)>	6.7	17.9	0.7
Completeness [%]	100.0	98.9	99.8
Redundancy	13.2	10.5	13.1
CC(1/2)	0.993	0.983	0.457

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	8.2	291	0.8 microliter of CRBN-DDB1 complex at 25 mg/mL (including 1 mM compound and 2 % DMSO final) plus 0.8 microliter of a crystallisation solution consisting of 0.1 M Hepes pH 8.2, 0.2 M NaCl and 10-16 % PEG Smear Medium, plus 0.2 microliter of seeds (established from the same conditions), against 500 microliter of crystallisation solution.