9IOW | pdb_00009iow

Crystal Structure of SME-1 E166A Mutant in complex with Cefaclor

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
1.86	34.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.297	α = 90
b = 50.788	β = 98.634
c = 61.91	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		2024-06-03	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	2.4	23.46	97	0.993	10.9	3.9		8331

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	2.4	2.49			0.925

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	21.476	8321	389	96.666	0.156	0.1509	0.151	0.2624	0.2649	22.131

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]
-0.526		0.49	-1.32		1.623

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.673
r_dihedral_angle_6_deg	14.599
r_dihedral_angle_2_deg	14.592
r_lrange_it	10.824
r_dihedral_angle_1_deg	8.306
r_scangle_it	5.782
r_rigid_bond_restr	5.205
r_mcangle_it	5.114
r_scbond_it	3.803
r_mcbond_it	3.167
r_angle_refined_deg	2.761
r_symmetry_nbd_refined	0.354
r_nbtor_refined	0.31
r_nbd_refined	0.242
r_symmetry_xyhbond_nbd_refined	0.209
r_chiral_restr	0.189
r_xyhbond_nbd_refined	0.16
r_bond_refined_d	0.014
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2058
Nucleic Acid Atoms
Solvent Atoms	43
Heterogen Atoms	26

Software

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