9IO7 | pdb_00009io7

Crystal Structure of SME-1 Carbapenemase in complex with Zidebactam

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, 0.2M lithium chloride

Crystal Properties
Matthews coefficient	Solvent content
1.84	33.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.884	α = 90
b = 50.18	β = 97.939
c = 60.586	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		2024-06-19	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	2.4	23.159	99.9	0.997	15.9	8.3		8470

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	2.4	2.49			0.972

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	2.4	23.159	8453	418	99.764	0.187	0.1833	0.1826	0.2668	0.2666	20.373

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]
-2.893		0.216	0.143		2.589

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.488
r_dihedral_angle_2_deg	14.165
r_dihedral_angle_6_deg	13.505
r_dihedral_angle_1_deg	6.881
r_lrange_it	6.588
r_rigid_bond_restr	3.428
r_scangle_it	2.542
r_mcangle_it	2.351
r_angle_refined_deg	1.927
r_scbond_it	1.57
r_mcbond_it	1.394
r_symmetry_xyhbond_nbd_refined	0.508
r_nbtor_refined	0.305
r_symmetry_nbd_refined	0.27
r_nbd_refined	0.222
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.126
r_bond_refined_d	0.008
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2058
Nucleic Acid Atoms
Solvent Atoms	36
Heterogen Atoms	30

Software

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