9HLN

Crystal structure of MnmA D100C mutant from Streptococcus pneumoniae with [4Fe-4S] cluster in complex with formate

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SOLEIL BEAMLINE PROXIMA 2
Synchrotron site	SOLEIL
Beamline	PROXIMA 2
Temperature [K]	100
Detector technology	PIXEL
Collection date	2023-03-08
Detector	DECTRIS EIGER X 9M
Wavelength(s)	0.980
Spacegroup name	P 32 2 1
Unit cell lengths	93.452, 93.452, 159.020
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	19.810 - 1.920
R-factor	0.1636
Rwork	0.162
R-free	0.18960
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.006
RMSD bond angle	0.831
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]	19.810	19.809	2.133
High resolution limit [Å]	1.920	6.137	1.922
Rmerge	0.215	0.084	1.419
Rmeas	0.220	0.086	1.456
Rpim	0.049	0.019	0.325
Total number of observations		40103	39866
Number of reflections	39900	1995	1995
<I/σ(I)>	10.73	28.53	2.12
Completeness [%]	94.8	100	75.8
Completeness (spherical) [%]		100.0	12.2
Completeness (ellipsoidal) [%]		100.0	75.8
Redundancy	20.45	20.1	19.98
CC(1/2)	0.998	0.999	0.888
Anomalous completeness (spherical)		100.0	11.3
Anomalous completeness		100.0	76.4
Anomalous redundancy		11.4	10.7
CC(ano)		0.367	-0.037
|DANO|/σ(DANO)		1.1	0.7

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	7	293	ANAEROBY (<1.5 ppm O2) 3.5M Sodium formate 0.1M Bis-tris propane pH 7.0