5M3C

Structure of the hybrid domain (GGDEF-EAL) of PA0575 from Pseudomonas aeruginosa PAO1 at 2.8 Ang. with GTP and Ca2+ bound to the active site of the GGDEF domain

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		294	Protein solution: 3 mg/ml in 20 mM Tris pH 7.6, 150 mM, CaCl2 2,5mM, GTP 0.32 mM mixing volumes 1 microL (1:1) Reservoir: PEG 4K 2%, CaCl2 0,01M, KCl 0,05 M, sodium cacodilato pH 6 0,05M Cryo-protection:PEG 4K raised to 3%, addition of 20% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.307	α = 90
b = 133.931	β = 90
c = 69.141	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX SX-165mm		2016-06-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.3	0.894	BESSY	14.3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.8	48.1	99.9	0.147	0.998	14.6	8.1		28700			55.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.95	99.7		1.342	0.74		8.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4RNJ, 4IOB	2.8	48.1	27257	1388	99.79	0.2452	0.2436	0.2773	RANDOM	61.268

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]
-4.84			2.6		2.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.066
r_dihedral_angle_4_deg	17.128
r_dihedral_angle_3_deg	16.47
r_dihedral_angle_1_deg	3.996
r_mcangle_it	2.202
r_mcbond_it	1.226
r_mcbond_other	1.226
r_angle_refined_deg	0.741
r_angle_other_deg	0.543
r_chiral_restr	0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.066
r_dihedral_angle_4_deg	17.128
r_dihedral_angle_3_deg	16.47
r_dihedral_angle_1_deg	3.996
r_mcangle_it	2.202
r_mcbond_it	1.226
r_mcbond_other	1.226
r_angle_refined_deg	0.741
r_angle_other_deg	0.543
r_chiral_restr	0.04
r_bond_refined_d	0.003
r_gen_planes_refined	0.002
r_bond_other_d
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6411
Nucleic Acid Atoms
Solvent Atoms	15
Heterogen Atoms	69

Software

Software
Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.