9JNB | pdb_00009jnb

Crystal Structure of SME-1 E166A mutant in complex with imipenem

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
1.92	35.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.847	α = 90
b = 50.915	β = 98.935
c = 60.835	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		2024-07-15	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	25.3	99.8	0.996	13.7	7		11402

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			0.937

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	23.452	11402	534	99.642	0.203	0.1996	0.2012	0.2826	0.2851	21.38

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]
-0.645		-1.659	1.216		-0.047

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.021
r_lrange_it	13.43
r_dihedral_angle_6_deg	13.259
r_dihedral_angle_2_deg	9.498
r_scangle_it	8.182
r_dihedral_angle_1_deg	7.183
r_mcangle_it	7.042
r_scbond_it	5.299
r_mcbond_it	4.397
r_rigid_bond_restr	3.413
r_angle_refined_deg	1.67
r_symmetry_xyhbond_nbd_refined	0.324
r_nbtor_refined	0.305
r_symmetry_nbd_refined	0.23
r_nbd_refined	0.223
r_xyhbond_nbd_refined	0.203
r_chiral_restr	0.114
r_gen_planes_refined	0.007
r_bond_refined_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2054
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms	20

Software

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