7AU1 | pdb_00007au1

Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (Compound 12)

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
2.12	41.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.038	α = 90
b = 81.925	β = 90
c = 88.241	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)	Rrim I (All)	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	1.36	60.039	91.7	0.072	0.077	0.026	0.999	15.1	8.1		69775

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.36	1.491	62.5		0.85	0.935	0.381		5.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6HZR	1.36	60.039	69775	3465	65.603	0.147	0.1445	0.15	0.2035	0.2	20.581

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]
-1.72			-1.212		2.933

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.549
r_dihedral_angle_4_deg	20.404
r_dihedral_angle_3_deg	13.65
r_rigid_bond_restr	10.267
r_dihedral_angle_1_deg	6.748
r_lrange_it	5.183
r_lrange_other	5.12
r_scangle_it	4.943
r_scangle_other	4.942
r_scbond_other	4.261
r_scbond_it	4.258
r_mcangle_it	3.602
r_mcangle_other	3.602
r_mcbond_other	3.094
r_mcbond_it	3.093
r_angle_refined_deg	1.924
r_angle_other_deg	1.462
r_symmetry_nbd_refined	0.33
r_nbd_other	0.288
r_symmetry_xyhbond_nbd_refined	0.233
r_nbd_refined	0.219
r_symmetry_nbd_other	0.192
r_xyhbond_nbd_refined	0.172
r_nbtor_refined	0.167
r_xyhbond_nbd_other	0.161
r_chiral_restr	0.097
r_symmetry_nbtor_other	0.085
r_symmetry_xyhbond_nbd_other	0.066
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3795
Nucleic Acid Atoms
Solvent Atoms	400
Heterogen Atoms	85

Software

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