9UJ9 | pdb_00009uj9

Crystal structure of SME-1 E166A in complex with cefotaxime

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, SITTING DROP		298	0.2 M lithium chloride, 20% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.481	α = 90
b = 51.5	β = 113.938
c = 77.024	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		2024-10-30	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	2.16	23.96	99.9	0.996	10.5	8.7		20261

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	2.16	2.23			0.887

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	21.981	20261	972	99.724	0.208	0.2053	0.2049	0.2715	0.281	24.909

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]
-4.304		-2.241	-3.453		6.991

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	44.538
r_dihedral_angle_3_deg	17.294
r_dihedral_angle_6_deg	14.035
r_dihedral_angle_2_deg	12.477
r_scangle_it	8.834
r_mcangle_it	7.828
r_dihedral_angle_1_deg	7.367
r_rigid_bond_restr	6.735
r_scbond_it	5.923
r_mcbond_it	4.974
r_angle_refined_deg	1.846
r_symmetry_xyhbond_nbd_refined	0.359
r_nbtor_refined	0.309
r_symmetry_nbd_refined	0.237
r_xyhbond_nbd_refined	0.235
r_nbd_refined	0.232
r_chiral_restr	0.127
r_ncsr_local_group_1	0.053
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	88
Heterogen Atoms	52

Software

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