9RFQ

Structure of liver pyruvate kinase in complex with Liver pyruvate kinase in complex with fluorescent probe I

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	2024-10-09
Detector	DECTRIS EIGER2 X 16M
Wavelength(s)	0.9763
Spacegroup name	C 1 2 1
Unit cell lengths	207.363, 112.743, 187.803
Unit cell angles	90.00, 91.83, 90.00

Refinement procedure

Resolution	187.710 - 2.385
R-factor	0.2106
Rwork	0.209
R-free	0.24170
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.007
RMSD bond angle	0.880
Data reduction software	XDS (Jun 30, 2023)
Data scaling software	Aimless (0.7.15)
Phasing software	PHASER
Refinement software	BUSTER (2.10.4)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	103.629	103.629	2.846
High resolution limit [Å]	2.385	8.359	2.385
Rmerge	0.239	0.062	1.192
Rmeas	0.258	0.067	1.294
Rpim	0.095	0.025	0.497
Total number of observations	596569	30181	26961
Number of reflections	83049	4152	4152
<I/σ(I)>	6.06	16.31	1.68
Completeness [%]	92.5	99.9	62
Completeness (spherical) [%]	48.3	99.9	5.9
Completeness (ellipsoidal) [%]	92.5	99.9	62.0
Redundancy	7.18	7.27	6.49
CC(1/2)	0.993	0.996	0.706
Anomalous completeness (spherical)	47.9	99.8	5.8
Anomalous completeness	92.4	99.8	62.4
Anomalous redundancy	3.7	3.9	3.3
CC(ano)	-0.097	-0.262	-0.038
|DANO|/σ(DANO)	0.8	0.7	0.8

Diffraction limits	Principal axes of ellipsoid fitted to diffraction cut-off surface
2.481 Å	0.792, 0.792, 0.792
2.902 Å	0.000, 0.000, 0.000
3.639 Å	0.610, 0.610, 0.610
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