9W7N | pdb_00009w7n

Crystal Structure of Vaborbactam in complex with SME-1 class A Carbapenemase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DY6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.2 M lithium chloride, 20% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.039	α = 90
b = 51.011	β = 92.799
c = 130.533	γ = 90

Symmetry
Space Group	P 1 21 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		2024-07-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

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	23.92	99.9	0.996	14.7	6.7		32253

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	2.05			0.898

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2	23.764	32240	1604	99.827	0.188	0.1849	0.1804	0.2418	0.2423	14.347

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]
2.094		0.271	1.881		-3.983

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	27.084
r_dihedral_angle_3_deg	16.957
r_dihedral_angle_6_deg	13.859
r_dihedral_angle_2_deg	9.532
r_dihedral_angle_1_deg	6.879
r_rigid_bond_restr	5.36
r_scangle_it	4.519
r_mcangle_it	3.721
r_scbond_it	2.97
r_mcbond_it	2.268
r_angle_refined_deg	1.928
r_nbtor_refined	0.309
r_symmetry_nbd_refined	0.294
r_nbd_refined	0.226
r_symmetry_xyhbond_nbd_refined	0.219
r_xyhbond_nbd_refined	0.192
r_chiral_restr	0.126
r_gen_planes_refined	0.008
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4123
Nucleic Acid Atoms
Solvent Atoms	237
Heterogen Atoms	70

Software

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