7ATM | pdb_00007atm

Structure of P. aeruginosa PBP3 in complex with a phenyl boronic acid (Compound 1)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6R3X

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.845	α = 90
b = 80.951	β = 90
c = 88.8	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	2018-10-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97624	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	1.58	59.824	95.3	0.065	0.024	0.999	15.8	8.7		53811

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	1.58	1.715	62.9		1.413	0.524	0.542	1.5	8.2

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6R3X	1.582	59.82	53811	2621	95.3	0.1922	0.1907	0.2	0.2246	0.23	RANDOM	33.059

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]
0.39			-0.13		-0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.321
r_dihedral_angle_4_deg	20.89
r_dihedral_angle_3_deg	13.389
r_dihedral_angle_1_deg	6.951
r_angle_refined_deg	1.581
r_angle_other_deg	1.401
r_chiral_restr	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.321
r_dihedral_angle_4_deg	20.89
r_dihedral_angle_3_deg	13.389
r_dihedral_angle_1_deg	6.951
r_angle_refined_deg	1.581
r_angle_other_deg	1.401
r_chiral_restr	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3625
Nucleic Acid Atoms
Solvent Atoms	235
Heterogen Atoms	22

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.