7Q14

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
2.2946.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.398α = 90
b = 161.934β = 90.513
c = 107.782γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-09-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.976269DiamondI03

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
12.1580.9799.60.9917.36.7117282
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)
12.152.190.5851.1

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-VALUE4S2P2.1580.97117142589599.4890.2120.20980.249842.613
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]
-1.920.2934.44-2.524
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.154
r_dihedral_angle_4_deg15.578
r_dihedral_angle_3_deg13.661
r_lrange_other8.43
r_lrange_it8.427
r_dihedral_angle_1_deg6.603
r_scangle_it6.19
r_scangle_other6.19
r_mcangle_it6.104
r_mcangle_other6.104
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.154
r_dihedral_angle_4_deg15.578
r_dihedral_angle_3_deg13.661
r_lrange_other8.43
r_lrange_it8.427
r_dihedral_angle_1_deg6.603
r_scangle_it6.19
r_scangle_other6.19
r_mcangle_it6.104
r_mcangle_other6.104
r_mcbond_it4.174
r_mcbond_other4.173
r_scbond_it4.062
r_scbond_other4.062
r_angle_refined_deg1.464
r_angle_other_deg1.28
r_nbd_other0.266
r_symmetry_nbd_refined0.255
r_nbd_refined0.213
r_symmetry_xyhbond_nbd_refined0.188
r_symmetry_nbd_other0.174
r_nbtor_refined0.166
r_xyhbond_nbd_refined0.148
r_symmetry_nbtor_other0.075
r_symmetry_xyhbond_nbd_other0.075
r_chiral_restr0.069
r_ncsr_local_group_40.069
r_ncsr_local_group_60.068
r_ncsr_local_group_20.067
r_ncsr_local_group_30.063
r_ncsr_local_group_80.061
r_ncsr_local_group_230.061
r_ncsr_local_group_70.059
r_ncsr_local_group_120.059
r_ncsr_local_group_50.057
r_ncsr_local_group_100.057
r_ncsr_local_group_260.057
r_ncsr_local_group_110.056
r_ncsr_local_group_170.056
r_ncsr_local_group_190.055
r_ncsr_local_group_210.055
r_ncsr_local_group_180.053
r_ncsr_local_group_250.053
r_ncsr_local_group_130.052
r_ncsr_local_group_280.052
r_ncsr_local_group_10.051
r_ncsr_local_group_90.051
r_ncsr_local_group_160.051
r_ncsr_local_group_270.05
r_ncsr_local_group_140.049
r_ncsr_local_group_200.048
r_ncsr_local_group_150.045
r_ncsr_local_group_240.045
r_ncsr_local_group_220.041
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15784
Nucleic Acid Atoms
Solvent Atoms516
Heterogen Atoms232

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing