7L5T | pdb_00007l5t

Crystal Structure of the Oxacillin-hydrolyzing Class D Extended-spectrum Beta-lactamase OXA-14 from Pseudomonas aeruginosa in Complex with Covalently Bound Clavulanic Acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1E3U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		292	Protein: 8.0 mg/ml, 0.01M Tris pH 8.3; Screen - AmSO4 (F6): 0.1M Bicine pH 9.0, 2.4M Ammonium sulfate; Soak & Cryo: 50mM Clavulanic acid, 2M Lithium sulfate, 10 min

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.94	α = 90
b = 95.451	β = 90
c = 125.974	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	CCD	MARMOSAIC 300 mm CCD	Be	2020-05-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.88	30	100	0.071	0.071	0.077	0.031	0.998	25.3	6.2		48753		-3	25.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.88	1.91	100		0.841	0.841	0.916	0.36	0.848	2.8	6.3

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	THROUGHOUT	1E3U	1.88	29.91	46232	2457	99.83	0.1687	0.1672	0.18	0.196	0.21	RANDOM	31.172

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]
0.31			2.16		-2.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.311
r_dihedral_angle_4_deg	11.927
r_dihedral_angle_3_deg	9.87
r_dihedral_angle_1_deg	3.753
r_angle_refined_deg	1.321
r_angle_other_deg	0.373
r_chiral_restr	0.066
r_gen_planes_refined	0.055
r_gen_planes_other	0.05
r_bond_refined_d	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.311
r_dihedral_angle_4_deg	11.927
r_dihedral_angle_3_deg	9.87
r_dihedral_angle_1_deg	3.753
r_angle_refined_deg	1.321
r_angle_other_deg	0.373
r_chiral_restr	0.066
r_gen_planes_refined	0.055
r_gen_planes_other	0.05
r_bond_refined_d	0.006
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3902
Nucleic Acid Atoms
Solvent Atoms	358
Heterogen Atoms	116

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

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.