4ZJ3

Crystal structure of cephalexin bound acyl-enzyme intermediate of Val216AcrF mutant TEM1 beta-lactamase from Escherichia coli: E166N and V216AcrF mutant.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BTLPDB entry 1BTL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.82950.1M 2-(N-morpholino) ethanesulfonic acid (MES) pH 6.5, 15% PEG 20.000 and 15% PEG 550MME
Crystal Properties
Matthews coefficientSolvent content
2.141.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.29α = 90
b = 47.025β = 90
c = 128.309γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-04-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-11.127SSRLBL7-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.737.931000.11215.27.131711
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7999.90.8122.57.2

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 1BTL1.72530049159399.910.155660.153870.18838RANDOM16.99
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]
1.030.18-1.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.075
r_dihedral_angle_4_deg20.181
r_dihedral_angle_3_deg12.829
r_dihedral_angle_1_deg9.349
r_long_range_B_refined4.158
r_long_range_B_other3.849
r_scangle_other2.415
r_angle_refined_deg1.922
r_angle_other_deg1.586
r_scbond_it1.479
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.075
r_dihedral_angle_4_deg20.181
r_dihedral_angle_3_deg12.829
r_dihedral_angle_1_deg9.349
r_long_range_B_refined4.158
r_long_range_B_other3.849
r_scangle_other2.415
r_angle_refined_deg1.922
r_angle_other_deg1.586
r_scbond_it1.479
r_scbond_other1.478
r_mcangle_it1.25
r_mcangle_other1.25
r_mcbond_other0.789
r_mcbond_it0.788
r_chiral_restr0.112
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.004
r_gen_planes_other0.002
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2068
Nucleic Acid Atoms
Solvent Atoms307
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing