8QNZ

Crystal Structure of a Class D Carbapenemase Complexed with Hydrolyzed Imipenem


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5291HEPES pH 7.5 no Cl-, 11.6% PEG8000, 8% 1-BuOH mixed with the 10 mg/mL protein stock at 1:1 ratio.
Crystal Properties
Matthews coefficientSolvent content
2.3748.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.31α = 90
b = 105.965β = 90
c = 124.679γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2020-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.918381DiamondI04

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
11.5380.7498.30.9991213.6159414
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)
11.531.560.621.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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-VALUE1.5362.417159336799098.1330.1490.14630.198821.078
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]
2.363-0.705-1.659
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.462
r_dihedral_angle_4_deg15.495
r_dihedral_angle_3_deg12.638
r_dihedral_angle_1_deg6.012
r_lrange_it3.4
r_scangle_it3.202
r_scangle_other3.201
r_lrange_other3.196
r_scbond_it2.765
r_scbond_other2.765
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.462
r_dihedral_angle_4_deg15.495
r_dihedral_angle_3_deg12.638
r_dihedral_angle_1_deg6.012
r_lrange_it3.4
r_scangle_it3.202
r_scangle_other3.201
r_lrange_other3.196
r_scbond_it2.765
r_scbond_other2.765
r_mcangle_it2.252
r_mcangle_other2.252
r_rigid_bond_restr1.982
r_mcbond_it1.859
r_mcbond_other1.85
r_angle_refined_deg1.474
r_angle_other_deg1.443
r_symmetry_nbd_refined0.293
r_nbd_refined0.239
r_nbd_other0.198
r_symmetry_nbd_other0.175
r_nbtor_refined0.17
r_xyhbond_nbd_refined0.156
r_symmetry_xyhbond_nbd_refined0.138
r_symmetry_nbtor_other0.079
r_chiral_restr0.076
r_symmetry_xyhbond_nbd_other0.071
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8012
Nucleic Acid Atoms
Solvent Atoms1019
Heterogen Atoms79

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing