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Crystal structure of the class A carbapenemase KPC-2 at 1.6 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DY6 PDB entry 1DY6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 20% PEG 6000, 0.1 M KSCN, 0.1 M Sodium Acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.77 55.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.3 α = 90 b = 91.3 β = 112.6 c = 73.1 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 IMAGE PLATE MAR scanner 345 mm plate mirror 1, double crystal, mirror 2 2006-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.97900 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.6 19.76 96.5 0.05 21.54 3.3 86680 14.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.6 1.7 95.2 0.137 11.68 3 14100
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1DY6 1.6 19.76 82347 4335 100 0.18875 0.18758 0.1869 0.2108 0.2103 RANDOM 10.889
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] -0.02 -0.22 0.36 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.886 r_dihedral_angle_4_deg 15.125 r_dihedral_angle_3_deg 11.953 r_dihedral_angle_1_deg 5.478 r_sphericity_free 4.654 r_scangle_it 3.059 r_sphericity_bonded 2.353 r_scbond_it 2.125 r_mcangle_it 1.375 r_angle_refined_deg 1.255
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.886 r_dihedral_angle_4_deg 15.125 r_dihedral_angle_3_deg 11.953 r_dihedral_angle_1_deg 5.478 r_sphericity_free 4.654 r_scangle_it 3.059 r_sphericity_bonded 2.353 r_scbond_it 2.125 r_mcangle_it 1.375 r_angle_refined_deg 1.255 r_rigid_bond_restr 1.185 r_mcbond_it 0.936 r_nbtor_refined 0.304 r_nbd_refined 0.232 r_symmetry_vdw_refined 0.183 r_xyhbond_nbd_refined 0.096 r_chiral_restr 0.084 r_symmetry_hbond_refined 0.074 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3953 Nucleic Acid Atoms Solvent Atoms 306 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Xnemo data collection XDS data reduction XSCALE data scaling PHASER phasing