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Crystal structure of stabilized TEM-1 beta-lactamase variant v.13 carrying G238S mutation
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 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 2.12 41.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.83 α = 90 b = 46.18 β = 93.12 c = 34.41 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 Merge 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 1.45 34.36 91.3 0.046 27.7 6.77 265088 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.55 86.2 0.369 0.366 5.44 6.7
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 1.45 34.38 36964 1946 90.7 0.107 0.104 0.1225 0.148 0.1619 RANDOM 16.27
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] -0.08 0.14 -0.02 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.928 r_sphericity_free 25.324 r_dihedral_angle_4_deg 14.797 r_dihedral_angle_3_deg 14.745 r_sphericity_bonded 10.588 r_rigid_bond_restr 7.978 r_dihedral_angle_1_deg 6.691 r_long_range_B_refined 5.136 r_long_range_B_other 4.742 r_scangle_other 4.054
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.928 r_sphericity_free 25.324 r_dihedral_angle_4_deg 14.797 r_dihedral_angle_3_deg 14.745 r_sphericity_bonded 10.588 r_rigid_bond_restr 7.978 r_dihedral_angle_1_deg 6.691 r_long_range_B_refined 5.136 r_long_range_B_other 4.742 r_scangle_other 4.054 r_scbond_other 3.863 r_scbond_it 3.852 r_mcangle_it 3.229 r_mcangle_other 3.229 r_mcbond_other 2.752 r_mcbond_it 2.751 r_angle_refined_deg 2.09 r_angle_other_deg 1.064 r_chiral_restr 0.154 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 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 2017 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 19
Software Software Software Name Purpose StructureStudio data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling