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Crystal Structure of a Class D Carbapenemase Complexed with Hydrolyzed Oxacillin
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 291 0.1M HEPES pH 8.0, 10% PEG 8000, 10% 1-BUTANOL mixed with the 10 mg/mL protein stock at 1:1 ratio.
Crystal Properties Matthews coefficient Solvent content 2.71 54.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.053 α = 90 b = 126.902 β = 98.289 c = 111.201 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 100 CCD ADSC QUANTUM 315r 2020-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.979150 SSRF BL17U1
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 1.85 19.81 99.9 0.997 10 6.9 109814
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 1.85 1.88 0.725 1.2
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 1.85 19.807 109782 5465 99.864 0.175 0.1731 0.1721 0.2111 0.2106 27.894
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] 3.963 0.53 -2.548 -1.505
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.164 r_dihedral_angle_4_deg 17.442 r_dihedral_angle_3_deg 13.699 r_dihedral_angle_1_deg 6.039 r_lrange_it 5.858 r_lrange_other 5.778 r_scangle_it 4.775 r_scangle_other 4.775 r_scbond_it 3.092 r_scbond_other 3.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.164 r_dihedral_angle_4_deg 17.442 r_dihedral_angle_3_deg 13.699 r_dihedral_angle_1_deg 6.039 r_lrange_it 5.858 r_lrange_other 5.778 r_scangle_it 4.775 r_scangle_other 4.775 r_scbond_it 3.092 r_scbond_other 3.092 r_mcangle_it 2.92 r_mcangle_other 2.919 r_mcbond_it 2.11 r_mcbond_other 2.109 r_angle_refined_deg 1.631 r_angle_other_deg 1.31 r_nbd_other 0.297 r_nbd_refined 0.205 r_symmetry_nbd_refined 0.179 r_symmetry_xyhbond_nbd_refined 0.165 r_symmetry_nbd_other 0.162 r_nbtor_refined 0.158 r_xyhbond_nbd_refined 0.15 r_chiral_restr_other 0.09 r_chiral_restr 0.081 r_symmetry_nbtor_other 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7932 Nucleic Acid Atoms Solvent Atoms 703 Heterogen Atoms 167
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing