Experiment: 6YBU

Crystal structure of a native BcsE (349-523) RQ complex with c-di-GMP and ATP bound

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6YAR	6YAR, 6TJ0
experimental model	PDB	6TJ0	6YAR, 6TJ0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277.4	100 mM Tris-HCl pH 9.0, 22-25% PEG 6000, 500 mM LiCl

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.99	α = 90
b = 72.57	β = 98.37
c = 161.25	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 X 9M		2017-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.980057954788	SOLEIL	PROXIMA 2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.49	50	98.5	0.995	11.45	6.9		86110			52.41

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.49	2.64	91.4		0.542	1.26	6.77

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6YAR, 6TJ0	2.49	47.71	1.34	86096	4331	98.76	0.1831	0.1808	0.1838	0.2249	0.2272	61.92

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.6166
f_angle_d	0.4901
f_chiral_restr	0.0381
f_plane_restr	0.0031
f_bond_d	0.0021

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13815
Nucleic Acid Atoms
Solvent Atoms	227
Heterogen Atoms	496

Software

Software
Software Name	Purpose
PHENIX	refinement
Coot	model building
PHASER	phasing
XDS	data scaling
XDS	data processing
XDS	data reduction