10YM

Crystal structure of a computationally designed protein bound to a Mn-containing cofactor (L1-dnMSBP)

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	ALS BEAMLINE 5.0.2
Synchrotron site	ALS
Beamline	5.0.2
Temperature [K]	100
Detector technology	PIXEL
Collection date	2022-12-18
Detector	DECTRIS PILATUS3 6M
Wavelength(s)	1
Spacegroup name	P 21 21 21
Unit cell lengths	46.651, 50.176, 84.876
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	43.190 - 1.500
R-factor	0.1645
Rwork	0.163
R-free	0.19790
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.011
RMSD bond angle	1.163
Data reduction software	xia2
Data scaling software	xia2
Phasing software	PHENIX (1.20.1_4487)
Refinement software	PHENIX (1.20.1_4487)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	43.190	1.554
High resolution limit [Å]	1.500	1.500
Rmerge	0.071	0.380
Rmeas	0.078	0.415
Rpim	0.030	0.166
Number of reflections	32611	3213
<I/σ(I)>	11.44	0.95
Completeness [%]	99.8
Redundancy	6.3
CC(1/2)	0.999	0.918

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP		296	700 uM L1-dnMSBP in 25 mM Tris buffer at pH 8 containing 300 mM NaCl was mixed with 20 mM ammonium phosphate monobasic buffer at pH 4.0 with 11-16% w/v PEG 3350 at a 1.5 uL : 1.5 uL mixing ratio under room temperature.