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Crystal structure of stabilized TEM-1 beta-lactamase variant v.13 carrying R164S mutation in complex with boron-based inhibitor EC25
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 293 9% (wt/vol) polyethylene glycol (PEG) 8000, 100 mM MES pH 6.2, and 200mM Ca(OAc)2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 44.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 155.54 α = 90 b = 47.03 β = 92.5 c = 34.62 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 1.54178
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 1.7 45.01 88380 25519 2 3
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 1.7 45.01 24240 1276 92.09 0.18923 0.18696 0.1867 0.23277 0.2324 RANDOM 15.89
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.362 r_dihedral_angle_4_deg 14.65 r_dihedral_angle_3_deg 13.071 r_long_range_B_refined 7.603 r_long_range_B_other 7.178 r_dihedral_angle_1_deg 5.322 r_scangle_other 3.614 r_mcangle_other 2.871 r_mcangle_it 2.673 r_scbond_other 2.388
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.362 r_dihedral_angle_4_deg 14.65 r_dihedral_angle_3_deg 13.071 r_long_range_B_refined 7.603 r_long_range_B_other 7.178 r_dihedral_angle_1_deg 5.322 r_scangle_other 3.614 r_mcangle_other 2.871 r_mcangle_it 2.673 r_scbond_other 2.388 r_scbond_it 2.349 r_mcbond_other 1.884 r_mcbond_it 1.739 r_angle_refined_deg 1.463 r_chiral_restr 0.069 r_gen_planes_refined 0.008 r_bond_refined_d 0.006 r_gen_planes_other 0.002 r_bond_other_d r_angle_other_deg 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2010 Nucleic Acid Atoms Solvent Atoms 367 Heterogen Atoms 30
Software Software Software Name Purpose StructureStudio data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling