4OPZ

Crystal structure of stabilized TEM-1 beta-lactamase variant v.13 carrying G238S mutation in complex with boron-based inhibitor EC25


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZG4pdb entry 1ZG4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.22939% (wt/vol) polyethylene glycol (PEG) 8000, 100 mM MES, and 200mM Ca(OAc)2, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.244.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 155.56α = 90
b = 47.04β = 92.46
c = 34.68γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.4531.15432083

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 REPLACEMENTTHROUGHOUTpdb entry 1ZG41.4531.17410472161970.1140.1120.159RANDOM15.25
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]
0.030.05-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free35.368
r_dihedral_angle_2_deg35.362
r_rigid_bond_restr20.314
r_dihedral_angle_3_deg12.387
r_sphericity_bonded11.653
r_dihedral_angle_4_deg10.614
r_dihedral_angle_1_deg5.487
r_long_range_B_refined5.161
r_scangle_other4.556
r_scbond_it4.471
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free35.368
r_dihedral_angle_2_deg35.362
r_rigid_bond_restr20.314
r_dihedral_angle_3_deg12.387
r_sphericity_bonded11.653
r_dihedral_angle_4_deg10.614
r_dihedral_angle_1_deg5.487
r_long_range_B_refined5.161
r_scangle_other4.556
r_scbond_it4.471
r_scbond_other4.455
r_long_range_B_other4.278
r_mcangle_it3.428
r_mcangle_other3.428
r_mcbond_other2.888
r_mcbond_it2.886
r_angle_refined_deg1.037
r_angle_other_deg0.627
r_chiral_restr0.061
r_gen_planes_refined0.006
r_bond_refined_d0.004
r_gen_planes_other0.004
r_bond_other_d0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2017
Nucleic Acid Atoms
Solvent Atoms379
Heterogen Atoms34

Software

Software
Software NamePurpose
StructureStudiodata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling