3C5A

Crystal structure of the C-terminal deleted mutant of the class A carbapenemase KPC-2 at 1.23 angstrom


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ODSPDB ENTRY 2ODS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP429120% PEG4K, 0.1M KSCN, 0.1M Citrate, VAPOR DIFFUSION, SITTING DROP, pH4.0, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.0439.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.89α = 90
b = 65.99β = 90
c = 72.13γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDADSC QUANTUM 315mirror 1, double crystal, mirror 22007-03-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.979ESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.2327.1797.722.5513.66519714.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.231.3191.90.1966.511.69747

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2ODS1.2327.176518832591000.1820.1810.196RANDOM11.796
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]
0.1-0.01-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.311
r_dihedral_angle_3_deg11.727
r_dihedral_angle_4_deg9.134
r_dihedral_angle_1_deg5.739
r_scangle_it2.07
r_scbond_it1.398
r_angle_refined_deg1.139
r_mcangle_it0.933
r_mcbond_it0.558
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.311
r_dihedral_angle_3_deg11.727
r_dihedral_angle_4_deg9.134
r_dihedral_angle_1_deg5.739
r_scangle_it2.07
r_scbond_it1.398
r_angle_refined_deg1.139
r_mcangle_it0.933
r_mcbond_it0.558
r_nbtor_refined0.304
r_xyhbond_nbd_refined0.257
r_nbd_refined0.217
r_symmetry_vdw_refined0.198
r_chiral_restr0.072
r_symmetry_hbond_refined0.067
r_bond_refined_d0.006
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1972
Nucleic Acid Atoms
Solvent Atoms183
Heterogen Atoms13

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Xnemodata collection
XDSdata reduction
PHASERphasing