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Crystal Structure of a Class D Carbapenemase Complexed with Imipenem
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4S2P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 HEPES 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 coefficient Solvent content 2.31 46.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.42 α = 90 b = 107.6 β = 90 c = 124.59 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 100 PIXEL DECTRIS EIGER2 X 16M 2020-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.918380 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.1 49.39 99.9 0.998 8.2 13.6 66086
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 0.695 1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4S2P 2.1 49.39 66012 3258 99.853 0.243 0.2408 0.2359 0.2778 0.2736 36.852
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.89 r_dihedral_angle_4_deg 16.666 r_dihedral_angle_3_deg 14.607 r_dihedral_angle_1_deg 6.624 r_lrange_it 6.44 r_lrange_other 6.433 r_scangle_it 5.007 r_scangle_other 5.007 r_mcangle_it 4.306 r_mcangle_other 4.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.89 r_dihedral_angle_4_deg 16.666 r_dihedral_angle_3_deg 14.607 r_dihedral_angle_1_deg 6.624 r_lrange_it 6.44 r_lrange_other 6.433 r_scangle_it 5.007 r_scangle_other 5.007 r_mcangle_it 4.306 r_mcangle_other 4.306 r_scbond_it 3.375 r_scbond_other 3.375 r_mcbond_it 3.017 r_mcbond_other 3.016 r_angle_refined_deg 1.523 r_angle_other_deg 1.279 r_symmetry_nbd_refined 0.269 r_nbd_other 0.253 r_symmetry_xyhbond_nbd_refined 0.219 r_nbd_refined 0.217 r_symmetry_nbd_other 0.175 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.163 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.07 r_ncsr_local_group_2 0.054 r_ncsr_local_group_3 0.053 r_ncsr_local_group_4 0.053 r_ncsr_local_group_5 0.052 r_ncsr_local_group_6 0.051 r_ncsr_local_group_1 0.041 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7967 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing