6N9R

Structure of the Quorum Quenching lactonase from Parageobacillus caldoxylosilyticus bound to substrate 3-oxo-C12-AHL

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6N9I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		292	Concentrated protein samples 10mg.mL-1, ammonium sulfate 1 to 2.25M, 0.1M sodium acetate. Soaking in 20 mM of C12 AHL for 5 min. Diffraction quality crystals appeared after 1 d at 292 K

Crystal Properties
Matthews coefficient	Solvent content
2.86	57.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 145.01	α = 90
b = 108.59	β = 115.75
c = 78.6	γ = 90

Symmetry
Space Group	C 1 2 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 PILATUS 6M		2018-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.03333	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim 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	1.75	70.8	99.2	0.051	0.059	0.999	15.21	3.98		109519

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.85	99.5		0.419	0.48	0.947	3.32	4.07

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	6N9I	1.75	70.8	104043	5476	99.33	0.17894	0.17597	0.23481	RANDOM	23.912

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]
0.1		-0.05	-0.04		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.538
r_sphericity_free	26.558
r_sphericity_bonded	15.976
r_dihedral_angle_4_deg	14.388
r_dihedral_angle_3_deg	13.905
r_rigid_bond_restr	10.352
r_scangle_other	5.836
r_dihedral_angle_1_deg	5.65
r_long_range_B_refined	5.257
r_long_range_B_other	5.253
r_scbond_it	5.044
r_scbond_other	5.042
r_mcangle_other	3.888
r_mcangle_it	3.886
r_mcbond_it	3.376
r_mcbond_other	3.32
r_angle_other_deg	0.987
r_angle_refined_deg	0.595
r_chiral_restr	0.03
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_gen_planes_other	0.002
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6711
Nucleic Acid Atoms
Solvent Atoms	451
Heterogen Atoms	250

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing