9JNG | pdb_00009jng

Crystal Structure of SME-1 E166A mutant with Tebipenem

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
2.2	42.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.765	α = 90
b = 51.688	β = 114.222
c = 76.4	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		2024-07-22	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	2.26	24.23	99.9	0.992	8.1	7.1		24193

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	2.26	2.33			0.883	2.7

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	2.26	23.289	24161	1169	99.789	0.184	0.1793	0.1815	0.2696	0.2722	26.804

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]
-0.84		0.734	-3.312		2.486

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	18.214
r_dihedral_angle_3_deg	16.084
r_lrange_it	15.785
r_dihedral_angle_6_deg	14.464
r_scangle_it	10.058
r_mcangle_it	8.998
r_dihedral_angle_1_deg	7.107
r_scbond_it	6.711
r_mcbond_it	5.775
r_rigid_bond_restr	4.19
r_angle_refined_deg	1.948
r_symmetry_xyhbond_nbd_refined	0.454
r_nbtor_refined	0.308
r_symmetry_nbd_refined	0.3
r_nbd_refined	0.221
r_xyhbond_nbd_refined	0.159
r_chiral_restr	0.132
r_ncsr_local_group_1	0.055
r_bond_refined_d	0.008
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4108
Nucleic Acid Atoms
Solvent Atoms	134
Heterogen Atoms	70

Software

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