9UJ7 | pdb_00009uj7

Crystal Structure of SME-1 E166A in complex with cefoperazone

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		298	0.2 M Lithium Chloride, 20% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.594	α = 90
b = 51.352	β = 114.053
c = 77.997	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		2024-05-19	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	2.2	23.75	99.9	0.994	12.6	7.1		26555

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			0.744

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	23.183	26543	1274	99.842	0.166	0.1622	0.1622	0.2466	0.2467	20.956

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]
-0.496		0.331	-0.899		0.786

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	18.984
r_dihedral_angle_3_deg	18.19
r_dihedral_angle_6_deg	15.431
r_lrange_it	11.631
r_scangle_it	7.786
r_dihedral_angle_1_deg	7.294
r_rigid_bond_restr	6.987
r_mcangle_it	5.76
r_scbond_it	5.413
r_mcbond_it	3.741
r_angle_refined_deg	3.209
r_symmetry_nbd_refined	0.332
r_nbtor_refined	0.314
r_chiral_restr	0.308
r_nbd_refined	0.226
r_xyhbond_nbd_refined	0.194
r_ncsr_local_group_1	0.11
r_symmetry_xyhbond_nbd_refined	0.071
r_bond_refined_d	0.019
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4116
Nucleic Acid Atoms
Solvent Atoms	112
Heterogen Atoms	87

Software

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