7AU9

Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (Compound 14)

X-RAY DIFFRACTION

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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
2.17	43.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.7	α = 90
b = 82.724	β = 90
c = 88.538	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	2019-01-26	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	2.137	60.446	94.1	0.121	0.044	0.999	12.9	8.6		21028

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	2.137	2.341	67.2		1.311	0.499	0.582	1.6	7.8

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	2.137	60.446	21028	960	73.499	0.196	0.1919	0.2743	48.565

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]
0.193			-0.313		0.121

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.65
r_dihedral_angle_4_deg	20.769
r_dihedral_angle_3_deg	17.404
r_lrange_it	9.125
r_lrange_other	9.06
r_dihedral_angle_1_deg	7.636
r_scangle_it	6.468
r_scangle_other	6.467
r_mcangle_it	5.852
r_mcangle_other	5.848
r_scbond_it	4.179
r_scbond_other	4.178
r_mcbond_it	3.904
r_mcbond_other	3.903
r_angle_refined_deg	1.57
r_angle_other_deg	1.231
r_symmetry_xyhbond_nbd_refined	0.234
r_nbd_other	0.232
r_nbd_refined	0.219
r_symmetry_nbd_refined	0.214
r_symmetry_nbd_other	0.19
r_xyhbond_nbd_refined	0.164
r_nbtor_refined	0.163
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.063
r_symmetry_xyhbond_nbd_other	0.061
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	3731
Nucleic Acid Atoms
Solvent Atoms	97
Heterogen Atoms	32

Software

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