9HE2

Crystal structure of CyuA C289A mutant from Methanococcus maripaludis with [4Fe-4S] clusters in complex with ethylene glycol

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SOLEIL BEAMLINE PROXIMA 1
Synchrotron site	SOLEIL
Beamline	PROXIMA 1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2024-04-13
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.978
Spacegroup name	P 32 2 1
Unit cell lengths	74.632, 74.632, 251.059
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	19.900 - 3.740
R-factor	0.2197
Rwork	0.217
R-free	0.26270
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.003
RMSD bond angle	0.548
Data reduction software	XDS (Jun 30, 2024)
Data scaling software	STARANISO (2.4.16)
Phasing software	PHASER
Refinement software	PHENIX (1.21.2-5419)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	19.905	19.905	4.039
High resolution limit [Å]	3.738	10.684	3.738
Rmerge	0.145	0.048	1.604
Rmeas	0.152	0.051	1.685
Rpim	0.046	0.017	0.508
Total number of observations	80984	3516	3924
Number of reflections	7395	370	370
<I/σ(I)>	8.95	34.52	1.34
Completeness [%]	92.1	100	39.3
Completeness (spherical) [%]	83.1	100.0	20.5
Completeness (ellipsoidal) [%]	92.1	100.0	39.3
Redundancy	10.95	9.5	10.61
CC(1/2)	0.998	0.998	0.679
Anomalous completeness (spherical)	81.8	100.0	18.6
Anomalous completeness	91.7	100.0	37.1
Anomalous redundancy	6.1	6.0	6.1
CC(ano)	0.141	0.135	-0.030
|DANO|/σ(DANO)	0.8	1.2	0.7

Diffraction limits	Principal axes of ellipsoid fitted to diffraction cut-off surface
3.948 Å	1.000, 1.000, 1.000
3.948 Å	0.000, 0.000, 0.000
3.725 Å	0.000, 0.000, 0.000
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	5.5	292	ANAEROBY (<1.5 ppm O2) 12% w/v PEG 4000 0.1M tri-sodium citrate dihydrate pH 5.5 0.1M NaCl