9P0V

Structure of PYCR1 complexed with the allosteric inhibitor 7-benzamido-4-hydroxynaphthalene-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	2025-02-08
Detector	DECTRIS EIGER2 S 16M
Wavelength(s)	0.979200
Spacegroup name	C 1 2 1
Unit cell lengths	111.757, 180.373, 88.206
Unit cell angles	90.00, 106.46, 90.00

Refinement procedure

Resolution	42.040 - 1.800
R-factor	0.1747
Rwork	0.173
R-free	0.20110
Structure solution method	FOURIER SYNTHESIS
RMSD bond length	0.007
RMSD bond angle	0.867
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHENIX
Refinement software	PHENIX ((1.21.2_5419: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	92.140	1.830
High resolution limit [Å]	1.800	1.800
Rmerge	0.098	2.140
Rmeas	0.106	2.319
Rpim	0.040	0.882
Total number of observations		50097
Number of reflections	302248	7432
<I/σ(I)>	13.8	1.1
Completeness [%]	99.3
Redundancy	6.9	6.7
CC(1/2)	0.999	0.515

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		293	Resevoir contained 340 mM Li2SO4, 12% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 20 mM 7-benzamido-4-hydroxynaphthalene-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, 88 mM 7-benzamido-4-hydroxynaphthalene-2-sulfonic acid, and 15 mM (S)-(-)-2-Hydroxy-3,3-dimethylbutyric acid