9VGV | pdb_00009vgv

Crystal Structure of BlaA beta-lactamase in complex with the Antifungal Agent Tavaborole.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8IWV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M TRIS hydrochloride pH 8.5, 2.0 M Ammonium phosphate monobasic

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.494	α = 90
b = 72.98	β = 94.421
c = 43.938	γ = 90

Symmetry
Space Group	C 1 2 1

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	RIGAKU HyPix-6000HE		2024-08-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54184

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.5	24.44	99.9	0.998	7.8	6.2		10042

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.6	100		0.925

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	8IWV	2.5	23.516	10040	474	99.801	0.2	0.1966	0.1967	0.2694	0.2702	24.761

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]
2.364		0.147	-0.679		-1.687

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.177
r_dihedral_angle_6_deg	14.306
r_dihedral_angle_2_deg	9.762
r_dihedral_angle_1_deg	7.399
r_lrange_it	7.208
r_scangle_it	5.781
r_scbond_it	3.589
r_mcangle_it	3.314
r_angle_refined_deg	2.157
r_mcbond_it	2.075

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.177
r_dihedral_angle_6_deg	14.306
r_dihedral_angle_2_deg	9.762
r_dihedral_angle_1_deg	7.399
r_lrange_it	7.208
r_scangle_it	5.781
r_scbond_it	3.589
r_mcangle_it	3.314
r_angle_refined_deg	2.157
r_mcbond_it	2.075
r_nbtor_refined	0.317
r_nbd_refined	0.239
r_symmetry_nbd_refined	0.211
r_xyhbond_nbd_refined	0.182
r_chiral_restr	0.138
r_symmetry_xyhbond_nbd_refined	0.043
r_bond_refined_d	0.008
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1992
Nucleic Acid Atoms
Solvent Atoms	37
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
MOLREP	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.