9UJ8 | pdb_00009uj8

Crystal structure of SME-1 E166A with cefovecin

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	0.2M lithium chloride, 20% PEG4000

Crystal Properties
Matthews coefficient	Solvent content
1.8	31.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.295	α = 90
b = 50.596	β = 98.033
c = 60.34	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		2024-11-11	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)	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	2.1	21.54	99.2	0.997	11.2	4.9		12658

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	2.1	2.16			0.948

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	2.1	21.54	12642	587	98.789	0.18	0.1764	0.1778	0.2546	0.2556	24.88

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]
-5.385		-4.945	2.443		4.171

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	24.489
r_dihedral_angle_2_deg	21.313
r_dihedral_angle_3_deg	18.015
r_dihedral_angle_6_deg	14.2
r_scangle_it	10.039
r_mcangle_it	7.732
r_dihedral_angle_1_deg	6.879
r_scbond_it	6.744
r_rigid_bond_restr	6.37
r_mcbond_it	4.929
r_angle_refined_deg	1.965
r_symmetry_nbd_refined	0.465
r_nbtor_refined	0.307
r_symmetry_xyhbond_nbd_refined	0.296
r_nbd_refined	0.222
r_xyhbond_nbd_refined	0.201
r_chiral_restr	0.138
r_gen_planes_refined	0.008
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2054
Nucleic Acid Atoms
Solvent Atoms	71
Heterogen Atoms	30

Software

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