9D6Z

Crystal structure of Human Prostaglandin reductase 1 (PTGR1) in complex with methotrexate (Orthorhombic C form)

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	NSLS-II BEAMLINE 19-ID
Synchrotron site	NSLS-II
Beamline	19-ID
Temperature [K]	100
Detector technology	PIXEL
Collection date	2024-08-04
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.9786
Spacegroup name	C 2 2 21
Unit cell lengths	91.473, 98.209, 174.444
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	47.270 - 1.750
R-factor	0.1676
Rwork	0.166
R-free	0.19350
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.008
RMSD bond angle	0.926
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX (dev_5421)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	49.100	1.780
High resolution limit [Å]	1.750	1.750
Rmerge	0.174	1.574
Rmeas	0.181	1.639
Rpim	0.050	0.451
Total number of observations	1039140	55882
Number of reflections	79264	4303
<I/σ(I)>	9.9	1.8
Completeness [%]	100.0
Redundancy	13.1	13
CC(1/2)	0.996	0.658

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	Berkeley B2: 30% (w/v) PEG 3350, 100 mM Hepes free acid/ Sodium hydroxide pH 7.5, 400 mM Sodium chloride. HosaA.00871.a.A2.PW39298 at 16.1 mg/mL. His tag removed with 3C protease. 20 hour soak in 5mM methotrexate in crystallant. Plate01-Clover A2, Puck: PSL0602, Cryo: Direct.