7LJU

Porcine Dihydropyrimidine Dehydrogenase (DPD) crosslinked with 5-Ethynyluracil (5EU)

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 21-ID-D
Synchrotron site	APS
Beamline	21-ID-D
Temperature [K]	100
Detector technology	PIXEL
Collection date	2020-12-09
Detector	DECTRIS EIGER2 X 9M
Wavelength(s)	1.1272
Spacegroup name	P 1 21 1
Unit cell lengths	82.060, 158.940, 163.210
Unit cell angles	90.00, 96.03, 90.00

Refinement procedure

Resolution	40.590 - 1.870
R-factor	0.1739
Rwork	0.172
R-free	0.21090
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	1h7x
Data reduction software	xia2
Data scaling software	xia2
Phasing software	PHASER
Refinement software	PHENIX (1.19_4092)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	45.460	45.460	1.920
High resolution limit [Å]	1.870	8.360	1.870
Rmerge	0.215	0.069	1.066
Rpim	0.117	0.037	0.668
Number of reflections	336013	3888	23294
<I/σ(I)>	6.3	19	1.1
Completeness [%]	98.3	98.6	92.4
Redundancy	4.1	4.1	3.4
CC(1/2)	0.989	0.993	0.520

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP		293	DPD was crystallized by the vapor diffusion, hanging drop method by mixing 3 uL of 39 uM DPD in 25 mM HEPES, 2 mM DTT, 10% glycerol, pH 7.5 with 3 uL of well solution containing 100 mM NaCl, 2 mM DTT, 18% PEG 6000, pH 4.7. Rectangular hexahedron crystals grew in ~16-20 hours to a size of approximately 50 x 200 x 20 um. The crystals were soaked for 2 hours in 25 mM HEPES, 100 mM NaCl, 2 mM DTT, 100 uM NADPH, 100 uM 5EU, 20% PEG 6000, 20% PEG 400, pH 7.5. The whole procedure has been done anaerobically in the glove box.