7AU8

Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (Compound 13)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	25% (w/v) polyethylene glycol 3,350, 0.1M Bis-Tris propane pH 8 and 1% (w/v) protamine sulphate

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.996	α = 90
b = 82.871	β = 90
c = 88.735	γ = 90

Symmetry
Space Group	P 21 21 21

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 PILATUS3 6M	Mirrors	2019-04-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.79	60.57	94.9	0.07	0.025	0.999	16.7	9.1		35335

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.79	1.966	65.1		1.544	0.46	0.67		12

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6HZR	1.79	60.566	35335	1675	72.612	0.2	0.1969	0.2567	44.944

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]
0.325			-0.118		-0.207

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.824
r_dihedral_angle_4_deg	20.419
r_dihedral_angle_3_deg	16.049
r_lrange_it	7.945
r_lrange_other	7.912
r_dihedral_angle_1_deg	7.045
r_scangle_it	5.499
r_scangle_other	5.498
r_mcangle_it	5.325
r_mcangle_other	5.324
r_mcbond_it	3.513
r_mcbond_other	3.512
r_scbond_it	3.47
r_scbond_other	3.469
r_angle_refined_deg	1.485
r_angle_other_deg	1.241
r_nbd_refined	0.215
r_nbd_other	0.209
r_symmetry_xyhbond_nbd_refined	0.194
r_symmetry_nbd_other	0.184
r_symmetry_nbd_refined	0.173
r_xyhbond_nbd_refined	0.171
r_nbtor_refined	0.157
r_symmetry_xyhbond_nbd_other	0.113
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.067
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3735
Nucleic Acid Atoms
Solvent Atoms	218
Heterogen Atoms	27

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PHENIX	refinement
STARANISO	data processing
PDB_EXTRACT	data extraction