7AUB

Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (Compound 15)

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	25% (w/v) polyethylene glycol 3,350, 0.1M Bis-Tris propane pH 6 and 1% (w/v) protamine sulphate

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.256	α = 90
b = 82.977	β = 90
c = 89.089	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	2018-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

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	1.907	60.719	99.7	0.054	0.021	0.999	16.7	7.2		40602

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	1.907	1.94	98.3		1.654	0.702	0.366	0.9	6.4

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6HZR	1.907	60.719	40602	1968	99.674	0.201	0.1985	0.2456	51.936

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]
0.834			-0.872		0.038

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.798
r_dihedral_angle_4_deg	20.403
r_dihedral_angle_3_deg	16.364
r_lrange_other	9.881
r_lrange_it	9.874
r_scangle_it	7.326
r_scangle_other	7.324
r_dihedral_angle_1_deg	7.308
r_mcangle_it	6.473
r_mcangle_other	6.472
r_scbond_it	4.806
r_scbond_other	4.804
r_mcbond_other	4.629
r_mcbond_it	4.628
r_angle_refined_deg	1.541
r_angle_other_deg	1.293
r_nbd_refined	0.216
r_nbd_other	0.211
r_symmetry_nbd_other	0.179
r_symmetry_nbd_refined	0.162
r_nbtor_refined	0.161
r_xyhbond_nbd_refined	0.145
r_symmetry_xyhbond_nbd_refined	0.129
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.073
r_bond_refined_d	0.009
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	3657
Nucleic Acid Atoms
Solvent Atoms	151
Heterogen Atoms	21

Software

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