9KW9

Crystal structure of proline dipeptidase from Pyrococcus furiosus complexed with Co

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	RRCAT INDUS-2 BEAMLINE PX-BL21
Synchrotron site	RRCAT INDUS-2
Beamline	PX-BL21
Temperature [K]	100
Detector technology	CCD
Collection date	2024-11-09
Detector	MARMOSAIC 225 mm CCD
Wavelength(s)	0.97893
Spacegroup name	P 21 21 21
Unit cell lengths	56.471, 71.140, 163.531
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	38.900 - 2.100
R-factor	0.2254
Rwork	0.224
R-free	0.25490
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	AlphaFold
RMSD bond length	0.002
RMSD bond angle	0.554
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX (1.21.1_5286)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	46.470	2.160
High resolution limit [Å]	2.100	2.100
Rmerge	0.120	1.796
Rmeas	0.124
Rpim	0.033	0.483
Number of reflections	39365	3186
<I/σ(I)>	14.7	1.7
Completeness [%]	100.0	100
Redundancy	14.4	14.8
CC(1/2)	0.999	0.613

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	MICROBATCH	8	294.15	200 mM Sodium acetate trihydrate, 100 mM Bis-Tris propane (pH 8.5), 20% w/v PEG 3350, 20 mM Tris-Cl (pH 8.0), 200 mM NaCl (mixed in 1:1)