1DY6 | pdb_00001dy6

Structure of the imipenem-hydrolyzing beta-lactamase SME-1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BUE	MODIFIED NMC-A BETA-LACTAMASE (1BUE) SOFTWARE USED: AMORE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		PROTEIN WAS CRYSTALLIZED FROM 17% PEG 4000, 0.2 M AMMONIUM ACETATE, 0.1 M TRIS-HCL, PH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.26	40

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.5	α = 90
b = 51.72	β = 118.62
c = 71.69	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	291	DIFFRACTOMETER	ENRAF-NONIUS FAST			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR571

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	2.13	20	82	0.049		2.3		24447

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	MODIFIED NMC-A BETA-LACTAMASE (1BUE) SOFTWARE USED: AMORE	2.13	10	24447	2445	82	0.184	0.184	0.244	RANDOM	19.2

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]

RMS Deviations
Key	Refinement Restraint Deviation
x_angle_deg	1.44
x_bond_d	0.007
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d
x_improper_angle_d_na
x_improper_angle_d_prot
x_mcbond_it
x_mcangle_it
x_scbond_it
x_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4116
Nucleic Acid Atoms
Solvent Atoms	397
Heterogen Atoms

Software

Software
Software Name	Purpose
X-PLOR	refinement
MADNESS	data reduction
Agrovata	data scaling
X-PLOR	phasing