9R3H

Structure of liver pyruvate kinase in complex with fluorescent probe 4b

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	DIAMOND BEAMLINE I04
Synchrotron site	Diamond
Beamline	I04
Temperature [K]	100
Detector technology	PIXEL
Collection date	2023-03-14
Detector	DECTRIS EIGER2 X 16M
Wavelength(s)	0.95374
Spacegroup name	C 1 2 1
Unit cell lengths	208.521, 112.553, 189.315
Unit cell angles	90.00, 91.09, 90.00

Refinement procedure

Resolution	189.280 - 2.100
R-factor	0.206
Rwork	0.205
R-free	0.23330
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.008
RMSD bond angle	0.900
Data reduction software	XDS (Jan 10, 2022)
Data scaling software	Aimless (0.7.9)
Phasing software	PHASER
Refinement software	BUSTER (2.10.4)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	189.281	189.281	2.247
High resolution limit [Å]	2.100	6.158	2.100
Rmerge	0.161	0.049	1.757
Rmeas	0.173	0.053	1.889
Rpim	0.064	0.019	0.692
Total number of observations	1493667	74634	77473
Number of reflections	207434	10372	10372
<I/σ(I)>	7.4	19.14	1.45
Completeness [%]	93.8	100	55.4
Completeness (spherical) [%]	81.4	100.0	22.2
Completeness (ellipsoidal) [%]	93.8	100.0	55.4
Redundancy	7.2	7.2	7.47
CC(1/2)	0.995	0.998	0.534
Anomalous completeness (spherical)	81.3	99.7	22.2
Anomalous completeness	93.7	99.7	55.3
Anomalous redundancy	3.6	3.8	3.8
CC(ano)	-0.225	-0.485	-0.015
|DANO|/σ(DANO)	0.8	0.6	0.8

Diffraction limits	Principal axes of ellipsoid fitted to diffraction cut-off surface
2.100 Å	0.966, 0.966, 0.966
2.176 Å	0.000, 0.000, 0.000
2.363 Å	0.258, 0.258, 0.258
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