7PSF

Crystal Structure of a Class D Carbapenemase 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 DROP7.5291HEPES 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
2.3146.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.42α = 90
b = 107.6β = 90
c = 124.59γ = 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 I040.918380DiamondI04

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
12.149.3999.90.9988.213.666086
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)
12.12.150.6951

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-VALUE4S2P2.149.3966012325899.8530.2430.24080.277836.852
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]
4.549-0.138-4.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.89
r_dihedral_angle_4_deg16.666
r_dihedral_angle_3_deg14.607
r_dihedral_angle_1_deg6.624
r_lrange_it6.44
r_lrange_other6.433
r_scangle_it5.007
r_scangle_other5.007
r_mcangle_it4.306
r_mcangle_other4.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.89
r_dihedral_angle_4_deg16.666
r_dihedral_angle_3_deg14.607
r_dihedral_angle_1_deg6.624
r_lrange_it6.44
r_lrange_other6.433
r_scangle_it5.007
r_scangle_other5.007
r_mcangle_it4.306
r_mcangle_other4.306
r_scbond_it3.375
r_scbond_other3.375
r_mcbond_it3.017
r_mcbond_other3.016
r_angle_refined_deg1.523
r_angle_other_deg1.279
r_symmetry_nbd_refined0.269
r_nbd_other0.253
r_symmetry_xyhbond_nbd_refined0.219
r_nbd_refined0.217
r_symmetry_nbd_other0.175
r_nbtor_refined0.166
r_xyhbond_nbd_refined0.163
r_symmetry_nbtor_other0.077
r_chiral_restr0.07
r_ncsr_local_group_20.054
r_ncsr_local_group_30.053
r_ncsr_local_group_40.053
r_ncsr_local_group_50.052
r_ncsr_local_group_60.051
r_ncsr_local_group_10.041
r_bond_refined_d0.009
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 Atoms7967
Nucleic Acid Atoms
Solvent Atoms231
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing