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Room temperature crystal structure of stabilized TEM-1 beta-lactamase variant v.13 carrying G238S mutation
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 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 44.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.36 α = 90 b = 47.04 β = 92.63 c = 34.92 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 293 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 1.75 77.36 97 80712 16253 2 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1ZG4 1.95 44.99 16253 856 92.77 0.17951 0.17691 0.183 0.23016 0.2305 RANDOM 26.703
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] -0.11 0.21 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.019 r_dihedral_angle_4_deg 12.378 r_dihedral_angle_3_deg 12.07 r_long_range_B_refined 8.19 r_long_range_B_other 8.093 r_scangle_other 5.269 r_dihedral_angle_1_deg 4.071 r_mcangle_it 4.037 r_mcangle_other 4.036 r_scbond_it 3.463
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.019 r_dihedral_angle_4_deg 12.378 r_dihedral_angle_3_deg 12.07 r_long_range_B_refined 8.19 r_long_range_B_other 8.093 r_scangle_other 5.269 r_dihedral_angle_1_deg 4.071 r_mcangle_it 4.037 r_mcangle_other 4.036 r_scbond_it 3.463 r_scbond_other 3.458 r_mcbond_it 2.709 r_mcbond_other 2.708 r_angle_refined_deg 0.69 r_angle_other_deg 0.513 r_chiral_restr 0.043 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2017 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 19
Software Software Software Name Purpose StructureStudio data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling