7O5N

Crystal Structure of a Class D carbapenemase complexed with Avibactam


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4S2P 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82910.1M HEPES,pH=8.0, 10%PEG 8000, 4% 1-butanol, 10mM Avibactam, mixed with the 10 mg/mL protein stock at 1:1 ratio.
Crystal Properties
Matthews coefficientSolvent content
2.5251.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.749α = 90
b = 107.959β = 90
c = 125.675γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2019-04-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.979191SSRFBL17U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.681.8999.90.99912.113.2160843
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.630.7471.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4S2P1.673.144160736789499.8470.1890.1880.215733.332
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]
4.545-1.869-2.676
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.59
r_dihedral_angle_4_deg17.482
r_dihedral_angle_3_deg12.999
r_lrange_it6.297
r_lrange_other6.241
r_dihedral_angle_1_deg6.131
r_scangle_it5.336
r_scangle_other5.336
r_scbond_it3.605
r_scbond_other3.598
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.59
r_dihedral_angle_4_deg17.482
r_dihedral_angle_3_deg12.999
r_lrange_it6.297
r_lrange_other6.241
r_dihedral_angle_1_deg6.131
r_scangle_it5.336
r_scangle_other5.336
r_scbond_it3.605
r_scbond_other3.598
r_mcangle_it3.196
r_mcangle_other3.185
r_mcbond_it2.411
r_mcbond_other2.4
r_angle_refined_deg1.589
r_angle_other_deg1.438
r_chiral_restr_other0.226
r_nbd_refined0.216
r_nbd_other0.19
r_symmetry_nbd_other0.174
r_nbtor_refined0.172
r_symmetry_nbd_refined0.172
r_xyhbond_nbd_refined0.157
r_symmetry_xyhbond_nbd_refined0.149
r_symmetry_nbtor_other0.08
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7929
Nucleic Acid Atoms
Solvent Atoms692
Heterogen Atoms119

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing