7LJU | pdb_00007lju

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1H7X

Crystallization

Crystalization Experiments
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.

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.06	α = 90
b = 158.94	β = 96.03
c = 163.21	γ = 90

Symmetry
Space Group	P 1 21 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 EIGER2 X 9M		2020-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.1272	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.87	45.46	98.3	0.215	0.117	0.989	6.3	4.1		336013			21.49

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.87	1.92	92.4		1.066	0.668	0.52	1.1	3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1H7X	1.87	40.59	1.34	335874	16917	98.23	0.1739	0.1719	0.172	0.2109	0.2109	26.9761

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	30805
Nucleic Acid Atoms
Solvent Atoms	3389
Heterogen Atoms	676

Software

Software
Software Name	Purpose
PHENIX	refinement
xia2	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing