4ZAM

Crystal structure of SHV-1 beta-lactamase bound to avibactam


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529325% PEG6000, 100 mM Tris, pH 7.5, 0.56 mM Cymal-6
Crystal Properties
Matthews coefficientSolvent content
2.0238

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.398α = 90
b = 55.295β = 90
c = 85.366γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-08-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-11.1271SSRLBL7-1

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
11.425098.30.037273.544246
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)
11.421.4789.50.338

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT1.4236.8441966222699.260.167620.166270.19312RANDOM22.141
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
r_dihedral_angle_2_deg35.981
r_dihedral_angle_4_deg16.128
r_dihedral_angle_3_deg12.88
r_long_range_B_refined8.58
r_long_range_B_other8.512
r_scangle_other7.52
r_dihedral_angle_1_deg6.191
r_scbond_it5.74
r_scbond_other5.737
r_mcangle_it4.349
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.981
r_dihedral_angle_4_deg16.128
r_dihedral_angle_3_deg12.88
r_long_range_B_refined8.58
r_long_range_B_other8.512
r_scangle_other7.52
r_dihedral_angle_1_deg6.191
r_scbond_it5.74
r_scbond_other5.737
r_mcangle_it4.349
r_mcangle_other4.347
r_mcbond_it3.232
r_mcbond_other3.231
r_angle_refined_deg1.747
r_angle_other_deg0.953
r_chiral_restr0.206
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms2024
Nucleic Acid Atoms
Solvent Atoms283
Heterogen Atoms59

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing