9IO6 | pdb_00009io6

Crystal Structure of SME-1 Carbapenemase in complex with Nacubactam.

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	20% PEG 4000, 0.2 M Lithium Chloride

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.731	α = 90
b = 52.206	β = 114.549
c = 78.133	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		2024-06-12	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)	R Merge I (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	2.07	24.65	99.9	0.096	0.995	14.6	6.5		32338

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	2.07	2.13			0.821

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	2.07	24.65	32325	1640	99.907	0.181	0.1775	0.1778	0.2353	0.2356	18.505

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]
-1.154		-0.354	0.583		0.631

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.382
r_dihedral_angle_6_deg	14.512
r_lrange_it	9.547
r_dihedral_angle_2_deg	7.543
r_dihedral_angle_1_deg	6.612
r_scangle_it	3.377
r_rigid_bond_restr	2.722
r_mcangle_it	2.453
r_scbond_it	2.205
r_angle_refined_deg	1.813
r_mcbond_it	1.482
r_nbtor_refined	0.302
r_symmetry_nbd_refined	0.284
r_symmetry_xyhbond_nbd_refined	0.222
r_nbd_refined	0.213
r_xyhbond_nbd_refined	0.163
r_chiral_restr	0.121
r_ncsr_local_group_1	0.073
r_bond_refined_d	0.008
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4130
Nucleic Acid Atoms
Solvent Atoms	235
Heterogen Atoms	93

Software

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