9B2I

Structure of the quorum quenching lactonase GcL G156P mutant

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	1.0 - 1.25 M ammonium sulfate and 0.1 M sodium acetate pH 4.0 - 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 145.76	α = 90
b = 108.18	β = 116.13
c = 78.75	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 EIGER X 16M		2020-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.99184	APS	23-ID-B

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	2.35	64.83	97.6	0.998	13.23	4.01		45944

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	2.35	2.45			0.872	2.46

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.35	64.12	42485	2237	97.81	0.1921	0.1906	0.22061	RANDOM	52.157

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]
0.45		-3.45	3.99		-0.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.047
r_long_range_B_refined	9.972
r_long_range_B_other	9.971
r_dihedral_angle_2_deg	8.858
r_scangle_other	8.062
r_mcangle_it	6.067
r_mcangle_other	6.067
r_dihedral_angle_1_deg	5.491
r_scbond_it	5.385
r_scbond_other	5.385
r_mcbond_it	4.36
r_mcbond_other	4.355
r_angle_refined_deg	0.733
r_angle_other_deg	0.258
r_chiral_restr	0.036
r_gen_planes_refined	0.002
r_bond_refined_d	0.001
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6715
Nucleic Acid Atoms
Solvent Atoms	358
Heterogen Atoms	171

Software

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