9P0T

Structure of PYCR1 complexed with the allosteric inhibitor 4-hydroxy-7-(phenylamino)naphthalene-2-sulfonic acid in a remote site and NADH and (S)-(-)-2-Hydroxy-3,3-dimethylbutyric acid in the active site

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 24-ID-E
Synchrotron site	APS
Beamline	24-ID-E
Temperature [K]	100
Detector technology	PIXEL
Collection date	2025-03-12
Detector	DECTRIS EIGER2 S 9M
Wavelength(s)	0.97920
Spacegroup name	C 1 2 1
Unit cell lengths	112.540, 180.592, 88.109
Unit cell angles	90.00, 106.62, 90.00

Refinement procedure

Resolution	47.710 - 1.790
R-factor	0.1968
Rwork	0.195
R-free	0.22300
Structure solution method	FOURIER SYNTHESIS
RMSD bond length	0.007
RMSD bond angle	0.892
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHENIX (1.21.2_5419)
Refinement software	PHENIX ((1.21.2_5419: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	92.590	1.820
High resolution limit [Å]	1.790	1.790
Rmerge	0.178	1.341
Rmeas	0.193	1.452
Rpim	0.073	0.551
Total number of observations		51573
Number of reflections	307049	7630
<I/σ(I)>	9.2	1.6
Completeness [%]	98.7
Redundancy	6.8	6.8
CC(1/2)	0.995	0.229

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		293	Resevoir contained 400 mM Li2SO4, 13% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 22 mM 4-hydroxy-7-(phenylamino)naphthalene-2-sulfonic acid, 3.5 mM NADH, and 10 mM (S)-(-)-2-Hydroxy-3,3-dimethylbutyric acid. Crystal was soaked in cryobuffer containing 20% PEG 200 and 125 mM 4-hydroxy-7-(phenylamino)naphthalene-2-sulfonic acid