9RFT

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

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	2024-10-04
Detector	DECTRIS EIGER2 X 16M
Wavelength(s)	0.9763
Spacegroup name	C 1 2 1
Unit cell lengths	207.920, 112.965, 188.562
Unit cell angles	90.00, 91.44, 90.00

Refinement procedure

Resolution	188.500 - 2.274
R-factor	0.212
Rwork	0.210
R-free	0.24500
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.008
RMSD bond angle	0.890
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]	188.503	188.503	2.570
High resolution limit [Å]	2.274	7.156	2.274
Rmerge	0.131	0.036	1.316
Rmeas	0.141	0.038	1.413
Rpim	0.052	0.014	0.513
Total number of observations	946800	48886	50251
Number of reflections	132556	6628	6628
<I/σ(I)>	8.62	25.43	1.49
Completeness [%]	93.3	100	57
Completeness (spherical) [%]	66.2	100.0	10.8
Completeness (ellipsoidal) [%]	93.3	100.0	57.0
Redundancy	7.14	7.38	7.58
CC(1/2)	0.998	0.999	0.716
Anomalous completeness (spherical)	65.9	99.7	10.9
Anomalous completeness	93.2	99.7	57.9
Anomalous redundancy	3.6	3.9	3.8
CC(ano)	-0.009	-0.005	-0.016
|DANO|/σ(DANO)	0.8	0.7	0.7

Diffraction limits	Principal axes of ellipsoid fitted to diffraction cut-off surface
2.847 Å	0.811, 0.811, 0.811
2.507 Å	0.000, 0.000, 0.000
2.347 Å	-0.586, -0.586, -0.586
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