7PFN

Crystal Structure of a Class D Carbapenemase_K73ALY Complexed with Imipenem


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52910.1M HEPES pH 7.5, 11.6% PEG8000, 8% 1-BuOH, mixed with the 10 mg/mL protein stock at 1:1 ratio.
Crystal Properties
Matthews coefficientSolvent content
2.4249.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.799α = 90
b = 104.995β = 90
c = 124.745γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.976292DiamondI03

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
11.862.371000.9979.911.455552
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)
11.81.840.5881.1

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-VALUE4S2P1.862.3755487274599.9930.180.17780.213725.438
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]
1.4710.782-2.252
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.529
r_dihedral_angle_4_deg19.264
r_dihedral_angle_3_deg13.434
r_dihedral_angle_1_deg6.301
r_lrange_it5.75
r_lrange_other5.693
r_scangle_it4.728
r_scangle_other4.717
r_scbond_it3.069
r_scbond_other3.063
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.529
r_dihedral_angle_4_deg19.264
r_dihedral_angle_3_deg13.434
r_dihedral_angle_1_deg6.301
r_lrange_it5.75
r_lrange_other5.693
r_scangle_it4.728
r_scangle_other4.717
r_scbond_it3.069
r_scbond_other3.063
r_mcangle_it2.87
r_mcangle_other2.87
r_mcbond_it2.022
r_mcbond_other2.018
r_angle_refined_deg1.539
r_angle_other_deg1.395
r_nbd_refined0.213
r_symmetry_nbd_other0.171
r_nbtor_refined0.171
r_nbd_other0.164
r_xyhbond_nbd_refined0.14
r_symmetry_xyhbond_nbd_other0.122
r_symmetry_nbd_refined0.119
r_ncsr_local_group_10.106
r_symmetry_xyhbond_nbd_refined0.096
r_chiral_restr0.08
r_symmetry_nbtor_other0.077
r_bond_refined_d0.01
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 Atoms3975
Nucleic Acid Atoms
Solvent Atoms365
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing