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Crystal structure of the C-terminal deleted mutant of the class A carbapenemase KPC-2 at 1.23 angstrom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ODS PDB ENTRY 2ODS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 291 20% PEG4K, 0.1M KSCN, 0.1M Citrate, VAPOR DIFFUSION, SITTING DROP, pH4.0, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.04 39.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.89 α = 90 b = 65.99 β = 90 c = 72.13 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD ADSC QUANTUM 315 mirror 1, double crystal, mirror 2 2007-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.979 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.23 27.17 97.7 22.55 13.6 65197 14.7
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) 1.23 1.31 91.9 0.196 6.5 11.6 9747
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 2ODS 1.23 27.17 65188 3259 100 0.182 0.181 0.1649 0.196 0.1835 RANDOM 11.796
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.311 r_dihedral_angle_3_deg 11.727 r_dihedral_angle_4_deg 9.134 r_dihedral_angle_1_deg 5.739 r_scangle_it 2.07 r_scbond_it 1.398 r_angle_refined_deg 1.139 r_mcangle_it 0.933 r_mcbond_it 0.558 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.311 r_dihedral_angle_3_deg 11.727 r_dihedral_angle_4_deg 9.134 r_dihedral_angle_1_deg 5.739 r_scangle_it 2.07 r_scbond_it 1.398 r_angle_refined_deg 1.139 r_mcangle_it 0.933 r_mcbond_it 0.558 r_nbtor_refined 0.304 r_xyhbond_nbd_refined 0.257 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.198 r_chiral_restr 0.072 r_symmetry_hbond_refined 0.067 r_bond_refined_d 0.006 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1972 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 13
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction Xnemo data collection XDS data reduction PHASER phasing