9IL9 | pdb_00009il9

Crystal Structure of SME-1 carbapenemase in complex with Avibactam.

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, Lithium Chloride 0.2M

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.582	α = 90
b = 51.871	β = 114.112
c = 77.429	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		2024-06-11	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)	Rrim I (All)	Rpim I (All)	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	2.28	24.11	99.9	0.114	0.131	0.064	0.995	12.4	7.6		23927

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.28	24.11			0.037	0.043	0.021	0.999		6.7

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	2.28	23.18	23915	1154	99.858	0.159	0.1548	0.1544	0.2415	0.2443	16.815

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]
2.076		-0.595	0.505		-1.462

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.262
r_lrange_it	16.521
r_dihedral_angle_2_deg	15.527
r_dihedral_angle_6_deg	15.15
r_scangle_it	10.885
r_dihedral_angle_1_deg	8.871
r_scbond_it	7.671
r_rigid_bond_restr	7.361
r_mcangle_it	7.304
r_mcbond_it	4.684
r_angle_refined_deg	2.737
r_nbtor_refined	0.317
r_symmetry_nbd_refined	0.295
r_nbd_refined	0.236
r_symmetry_xyhbond_nbd_refined	0.217
r_xyhbond_nbd_refined	0.189
r_chiral_restr	0.172
r_bond_refined_d	0.014
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4120
Nucleic Acid Atoms
Solvent Atoms	183
Heterogen Atoms	65

Software

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