1DY6

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BUEMODIFIED NMC-A BETA-LACTAMASE (1BUE) SOFTWARE USED: AMORE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5PROTEIN WAS CRYSTALLIZED FROM 17% PEG 4000, 0.2 M AMMONIUM ACETATE, 0.1 M TRIS-HCL, PH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.2640

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.5α = 90
b = 51.72β = 118.62
c = 71.69γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray291DIFFRACTOMETERENRAF-NONIUS FASTMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR571

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.1320820.0492.324447

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTMODIFIED NMC-A BETA-LACTAMASE (1BUE) SOFTWARE USED: AMORE2.1310244472445820.1840.1840.244RANDOM19.2
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
KeyRefinement Restraint Deviation
x_angle_deg1.44
x_bond_d0.007
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
RMS Deviations
KeyRefinement Restraint Deviation
x_angle_deg1.44
x_bond_d0.007
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 AtomsNumber
Protein Atoms4116
Nucleic Acid Atoms
Solvent Atoms397
Heterogen Atoms

Software

Software
Software NamePurpose
X-PLORrefinement
MADNESSdata reduction
Agrovatadata scaling
X-PLORphasing