6TTS

Crystal structure of the GGDEF domain of DgcB from Caulobacter crescentus in complex with c-di-GMP

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SLS BEAMLINE X06SA
Synchrotron site	SLS
Beamline	X06SA
Temperature [K]	100
Detector technology	PIXEL
Collection date	2018-06-10
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.97947
Spacegroup name	P 41 2 2
Unit cell lengths	64.500, 64.500, 246.760
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	50.760 - 2.500
R-factor	0.2065
Rwork	0.203
R-free	0.26080
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	3ign 3hva 3qyy 3i5c 4wxw 3tvk 4urg 4zvf 4h54 4zmm 3icl 4iob 5euh 3ezu 4yme
RMSD bond length	0.010
RMSD bond angle	1.359
Data reduction software	iMOSFLM (7.2.2)
Data scaling software	Aimless (0.6.2)
Phasing software	PHASER (2.8.2)
Refinement software	PHENIX (1.13_2998)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	64.500	2.600
High resolution limit [Å]	2.500	2.500
Rmerge	0.159	0.515
Rmeas	0.183	0.672
Rpim	0.088	0.427
Number of reflections	19045	2068
<I/σ(I)>	8.3	2.3
Completeness [%]	99.9	99
Redundancy	7.2	3.7
CC(1/2)	0.813	0.693

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	0.2 M LiSO4, 0.1 M NaAcet pH 5.5, 8% w/v PEG 20k, 8% v/v PEG 500 MME, 500 uM c-di-GMP, 1 mM GTP