8U0I | pdb_00008u0i

Crystal structure of PA0012 complexed with cyclic-di-GMP from Pseudomonas aeruginosa

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	A0A6N0KW37

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	293.15	5.3 mg/mL PA0012 and 2.5 mM cyclic-di-GMP. 0.2 M NH4SO4, 15% (w/v) PEG4000, 0.1 M Tri-NaCit pH=5.6

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.317	α = 90
b = 50.317	β = 90
c = 90.596	γ = 90

Symmetry
Space Group	P 43 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	PIXEL	DECTRIS EIGER2 S 9M		2023-03-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.0004	ALS	8.2.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.54	43.99	100	0.081	0.083	0.013	1	19	39.2		17945			23.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.54	1.57	99.9		1.064	1.08	0.187	0.971		32.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.541	43.988	17885	873	99.989	0.175	0.1733	0.1734	0.2101	0.2105	RANDOM	27.158

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]
0.631			0.631		-1.262

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.98
r_dihedral_angle_3_deg	10.457
r_lrange_other	6.977
r_lrange_it	6.971
r_dihedral_angle_1_deg	6.885
r_scangle_it	5.714
r_scangle_other	5.709
r_dihedral_angle_2_deg	4.335
r_mcangle_it	3.931
r_mcangle_other	3.928
r_scbond_other	3.89
r_scbond_it	3.889
r_mcbond_it	2.629
r_mcbond_other	2.628
r_angle_refined_deg	2.048
r_angle_other_deg	0.744
r_dihedral_angle_other_2_deg	0.516
r_symmetry_nbd_refined	0.228
r_nbd_other	0.211
r_symmetry_nbd_other	0.195
r_nbd_refined	0.191
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.174
r_chiral_restr	0.113
r_symmetry_nbtor_other	0.093
r_symmetry_xyhbond_nbd_refined	0.087
r_bond_refined_d	0.012
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	663
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms	110

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
DIALS	data reduction
PHASER	phasing
Coot	model building