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Crystal structure of stabilized TEM-1 beta-lactamase variant v.13 carrying R164S/G238S mutation in complex with boron-based inhibitor EC25
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.2 293 9% (wt/vol) polyethylene glycol (PEG) 8000, 100 mM MES, and 200mM Ca(OAc)2, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.11 41.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.76 α = 90 b = 46.18 β = 92.72 c = 34.47 γ = 90
Symmetry Space Group C 1 2 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 IMAGE PLATE RIGAKU RAXIS IV++ M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
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 1.42 26.2 0.038 27.63 42706 3
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 1.42 1.6 89.5 0.14 10.86 5.62
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.42 26.2 40569 2136 93.9 0.1 0.098 0.1194 0.138 0.157 RANDOM 16.23
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 0.11 0.15 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.357 r_sphericity_free 24.078 r_dihedral_angle_4_deg 21.586 r_dihedral_angle_3_deg 14.426 r_sphericity_bonded 11.534 r_dihedral_angle_1_deg 7.237 r_rigid_bond_restr 6.531 r_long_range_B_refined 5.787 r_long_range_B_other 5.586 r_scangle_other 5.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.357 r_sphericity_free 24.078 r_dihedral_angle_4_deg 21.586 r_dihedral_angle_3_deg 14.426 r_sphericity_bonded 11.534 r_dihedral_angle_1_deg 7.237 r_rigid_bond_restr 6.531 r_long_range_B_refined 5.787 r_long_range_B_other 5.586 r_scangle_other 5.092 r_scbond_it 4.62 r_scbond_other 4.605 r_mcangle_it 3.77 r_mcangle_other 3.768 r_mcbond_other 3.497 r_mcbond_it 3.496 r_angle_refined_deg 2.044 r_angle_other_deg 1.039 r_chiral_restr 0.136 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2012 Nucleic Acid Atoms Solvent Atoms 283 Heterogen Atoms 37
Software Software Software Name Purpose StructureStudio data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling