9P1B

P. putida mandelate racemase co-crystallized with tavaborole

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 21-ID-G
Synchrotron site	APS
Beamline	21-ID-G
Temperature [K]	100
Detector technology	PIXEL
Collection date	2025-04-29
Detector	DECTRIS PILATUS 6M
Wavelength(s)	0.97856
Spacegroup name	I 4 2 2
Unit cell lengths	150.646, 150.646, 177.551
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	57.440 - 1.800
R-factor	0.2018
Rwork	0.200
R-free	0.23480
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.011
RMSD bond angle	1.043
Data reduction software	autoPROC
Data scaling software	autoPROC
Phasing software	PHASER
Refinement software	PHENIX (1.21.2_5419)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	114.870	1.833
High resolution limit [Å]	1.618	1.618
Rmerge	0.240	0.598
Rmeas	0.249	0.655
Rpim	0.063	0.257
Number of reflections	81806	4090
<I/σ(I)>	7.2	1.6
Completeness [%]	85.6	42
Redundancy	14.5	5.9
CC(1/2)	0.995	0.769

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	8	293	Reservoir solution: PEG3350 (9% w/v), HEPES (50mM; pH 8.0) Protein solution: mandelate racemase (10 mg/ml) + 500uM Tavaborole in 100mM HEPES, pH 7.5, 3.3mM MgCl2 2 uL of protein solution was mixed with 2 uL of well solution. Cube-like crystals grew spontaneously over 18-25 days. Crystals were equilibrated in synthetic stabilizing solution (10% w/v PEG3350, 50 mM HEPES, pH 8.0, 5 mM MgCl2, 500 uM Tavaborole, 5% v/v ethylene glycol) for 5 minutes and then transferred directly to cryoprotectant solution (10% w/v PEG3350, 50 mM HEPES, pH 8.0, 5 mM MgCl2, 500 uM Tavaborole, 20% v/v ethylene glycol) for 5 minutes prior to flash freezing in liquid nitrogen.