9R3M

Structure of liver pyruvate kinase in complex with fluorescent probe 8a

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	DIAMOND BEAMLINE I03
Synchrotron site	Diamond
Beamline	I03
Temperature [K]	100
Detector technology	PIXEL
Collection date	2023-11-20
Detector	DECTRIS EIGER2 XE 16M
Wavelength(s)	0.97629
Spacegroup name	C 1 2 1
Unit cell lengths	208.443, 112.896, 189.009
Unit cell angles	90.00, 91.06, 90.00

Refinement procedure

Resolution	188.980 - 2.062
R-factor	0.2005
Rwork	0.199
R-free	0.23480
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.008
RMSD bond angle	0.910
Data reduction software	XDS (Jun 30, 2023)
Data scaling software	Aimless (0.7.13)
Phasing software	PHASER
Refinement software	BUSTER (2.10.4)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	104.204	104.204	2.280
High resolution limit [Å]	2.062	6.411	2.062
Rmerge	0.127	0.038	1.162
Rmeas	0.137	0.041	1.258
Rpim	0.051	0.015	0.475
Total number of observations	1310724	68094	64815
Number of reflections	184428	9221	9221
<I/σ(I)>	9.89	31.26	1.52
Completeness [%]	91.3	100	65.4
Completeness (spherical) [%]	68.5	100.0	13.2
Completeness (ellipsoidal) [%]	91.3	100.0	65.4
Redundancy	7.11	7.38	7.03
CC(1/2)	0.998	0.999	0.995
Anomalous completeness (spherical)	68.1	99.8	13.1
Anomalous completeness	91.2	99.8	66.5
Anomalous redundancy	3.6	3.9	3.6
CC(ano)	-0.063	-0.131	-0.029
|DANO|/σ(DANO)	0.8	0.7	0.7

Diffraction limits	Principal axes of ellipsoid fitted to diffraction cut-off surface
2.057 Å	0.779, 0.779, 0.779
2.435 Å	0.000, 0.000, 0.000
2.363 Å	0.627, 0.627, 0.627
Criteria used in determination of diffraction limits	local <I/sigmaI> ≥ 1.2

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	100 mM HEPES/MOPS, 10% PEG8000, 20% ethylene glycol, 10 mM phenylalanine, 20 mM sodium oxalate