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Crystal structure of stabilized TEM-1 beta-lactamase variant v.13 carrying G238S mutation in complex with boron-based inhibitor EC25
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZG4 pdb entry 1ZG4
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 2.2 44.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 155.56 α = 90 b = 47.04 β = 92.46 c = 34.68 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) 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 1.45 31.15 43208 3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1ZG4 1.45 31.17 41047 2161 97 0.114 0.112 0.159 0.1601 RANDOM 15.25
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] 0.03 0.05 -0.05
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.368 r_dihedral_angle_2_deg 35.362 r_rigid_bond_restr 20.314 r_dihedral_angle_3_deg 12.387 r_sphericity_bonded 11.653 r_dihedral_angle_4_deg 10.614 r_dihedral_angle_1_deg 5.487 r_long_range_B_refined 5.161 r_scangle_other 4.556 r_scbond_it 4.471
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.368 r_dihedral_angle_2_deg 35.362 r_rigid_bond_restr 20.314 r_dihedral_angle_3_deg 12.387 r_sphericity_bonded 11.653 r_dihedral_angle_4_deg 10.614 r_dihedral_angle_1_deg 5.487 r_long_range_B_refined 5.161 r_scangle_other 4.556 r_scbond_it 4.471 r_scbond_other 4.455 r_long_range_B_other 4.278 r_mcangle_it 3.428 r_mcangle_other 3.428 r_mcbond_other 2.888 r_mcbond_it 2.886 r_angle_refined_deg 1.037 r_angle_other_deg 0.627 r_chiral_restr 0.061 r_gen_planes_refined 0.006 r_bond_refined_d 0.004 r_gen_planes_other 0.004 r_bond_other_d 0.002 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 2017 Nucleic Acid Atoms Solvent Atoms 379 Heterogen Atoms 34
Software Software Software Name Purpose StructureStudio data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling