9W7P | pdb_00009w7p

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

X-RAY DIFFRACTION

---

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, PEG 4000 20%

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.391	α = 90
b = 50.465	β = 97.722
c = 130.588	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		2024-12-30	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	2.2	21.78	99.9	0.994	8.9	7.5		24125

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	2.27			0.846

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	2.2	21.577	24098	1209	99.797	0.196	0.193	0.2009	0.2547	0.2575	16.836

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]
1.706		-0.156	-2.672		0.973

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	31.743
r_dihedral_angle_3_deg	17.791
r_dihedral_angle_2_deg	15.582
r_dihedral_angle_6_deg	13.401
r_scangle_it	7.287
r_dihedral_angle_1_deg	6.722
r_mcangle_it	5.557
r_scbond_it	4.761
r_rigid_bond_restr	4.571
r_mcbond_it	3.468
r_angle_refined_deg	1.786
r_nbtor_refined	0.306
r_symmetry_nbd_refined	0.244
r_nbd_refined	0.223
r_xyhbond_nbd_refined	0.193
r_chiral_restr	0.117
r_symmetry_xyhbond_nbd_refined	0.095
r_ncsr_local_group_1	0.045
r_bond_refined_d	0.008
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4116
Nucleic Acid Atoms
Solvent Atoms	164
Heterogen Atoms	39

Software

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