9SWV

Basic membrane protein D in complex with cytidine

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	ESRF BEAMLINE ID23-2
Synchrotron site	ESRF
Beamline	ID23-2
Temperature [K]	100
Detector technology	PIXEL
Collection date	2023-09-12
Detector	DECTRIS EIGER2 X 9M
Wavelength(s)	0.873130
Spacegroup name	P 1
Unit cell lengths	43.390, 57.490, 67.590
Unit cell angles	90.96, 108.59, 102.72

Refinement procedure

Resolution	40.180 - 1.250
Rwork	0.128
R-free	0.16440
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.010
RMSD bond angle	1.715
Data reduction software	XDS (VERSION Jun 30, 2023 BUILT=20230630)
Data scaling software	XSCALE (VERSION Jun 30, 2023 BUILT=20230630)
Phasing software	PHASER (2.8.3)
Refinement software	REFMAC (5.8.0425)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	40.180	40.180	1.270
High resolution limit [Å]	1.250	6.850	1.250
Rmerge	0.112	0.080	1.611
Rmeas	0.140	0.101	2.031
Rpim	0.083	0.060	1.211
Number of reflections	161460	993	6793
<I/σ(I)>	7.1	15.5	1.5
Completeness [%]	97.0	97.4	82.2
Redundancy	5	5.1	4.4
CC(1/2)	0.995	0.991	0.337

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		293	Protein solution (~20 mg/ml): 50 mM Tris pH 8.0; 1 mg/ml hygromycin A Well solution: 0.2 M CaCl2, 0.1 M NaAcetate pH 5.0, 20 % PEG6000 Seed stock from an earlier crystallization trial (may have contained very low levels of cytidine): 0.2 M CaCl2, 0.1M Tris pH 8.0, 22.5 % w/v PEG6000 Sitting drops: 90 nl of protein solution, 90 nl of well solution and 30 nl of seed stock. Cryo solution: 50% MPD were added to the drop to a final concentration of 16% (v/v).