6SP6

Ultra-high Resolution Crystal Structure of the CTX-M-15 Extended-Spectrum beta-Lactamase in Complex with Taniborbactam (VNRX-5133)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4HBT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	0.1M Tris-HCl, 2.2-2.4M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.558	α = 90
b = 45.719	β = 90
c = 117.219	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 2M		2015-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.966	ESRF	MASSIF-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.1	58.61	98.9	0.075	0.083	0.035	11.6	5.3	96837	96837

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)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.1	1.16	97.5		0.304	0.304	0.337	0.144	2.5	5.3

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4HBT	1.1	58.61	92020	4746	98.76	0.1026	0.1016	0.1208	RANDOM	12.099

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]
-0.01			-0.01		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	52.044
r_dihedral_angle_2_deg	37.272
r_sphericity_bonded	14.434
r_dihedral_angle_3_deg	11.969
r_dihedral_angle_4_deg	11.775
r_rigid_bond_restr	6.73
r_dihedral_angle_1_deg	5.9
r_angle_refined_deg	2.16
r_angle_other_deg	1.124
r_chiral_restr	0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	52.044
r_dihedral_angle_2_deg	37.272
r_sphericity_bonded	14.434
r_dihedral_angle_3_deg	11.969
r_dihedral_angle_4_deg	11.775
r_rigid_bond_restr	6.73
r_dihedral_angle_1_deg	5.9
r_angle_refined_deg	2.16
r_angle_other_deg	1.124
r_chiral_restr	0.15
r_bond_refined_d	0.025
r_gen_planes_refined	0.013
r_bond_other_d	0.005
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1957
Nucleic Acid Atoms
Solvent Atoms	261
Heterogen Atoms	71

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

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.