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Crystal structure of stabilized TEM-1 beta-lactamase variant v.13 carrying R164S mutation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZG4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.4 293 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 42.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.6 α = 90 b = 46.1 β = 93.3 c = 34.5 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 PIXEL DECTRIS PILATUS 6M M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.79990 ESRF ID29
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 1.05 44.15 97.2 0.036 16.45 3.31 360642 109005 2 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1ZG4 1.05 44.15 360642 103553 5451 97.17 0.13188 0.13054 0.14 0.15726 0.1667 RANDOM 13.864
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 0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.256 r_sphericity_free 31.677 r_dihedral_angle_3_deg 13.929 r_dihedral_angle_4_deg 12.962 r_sphericity_bonded 11.333 r_rigid_bond_restr 8.169 r_dihedral_angle_1_deg 7.395 r_long_range_B_refined 4.899 r_long_range_B_other 4.236 r_scbond_it 3.464
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.256 r_sphericity_free 31.677 r_dihedral_angle_3_deg 13.929 r_dihedral_angle_4_deg 12.962 r_sphericity_bonded 11.333 r_rigid_bond_restr 8.169 r_dihedral_angle_1_deg 7.395 r_long_range_B_refined 4.899 r_long_range_B_other 4.236 r_scbond_it 3.464 r_scangle_other 3.382 r_scbond_other 3.178 r_mcangle_it 2.411 r_angle_refined_deg 2.333 r_mcangle_other 2.152 r_mcbond_other 1.955 r_mcbond_it 1.954 r_angle_other_deg 1.358 r_chiral_restr 0.348 r_bond_refined_d 0.025 r_gen_planes_refined 0.011 r_gen_planes_other 0.005 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 2010 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 26
Software Software Software Name Purpose MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling