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Room temperature crystal structure of stabilized TEM-1 beta-lactamase variant v.13 carrying R164S/G238S mutations
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 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 2.26 45.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.9 α = 90 b = 47.2 β = 92.82 c = 34.89 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
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 1.7 45.15 93.1 0.063 12.72 92833 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.8 89.7 0.38 3.5
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 1ZG4 1.7 45.15 24685 1300 93.1 0.151 0.149 0.1482 0.189 0.1913 RANDOM 21.81
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] -0.05 0.01 0.01 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.225 r_dihedral_angle_4_deg 17.901 r_dihedral_angle_3_deg 15.483 r_long_range_B_refined 7.643 r_dihedral_angle_1_deg 6.287 r_mcangle_it 3.732 r_scbond_it 3.65 r_angle_refined_deg 2.455 r_mcbond_it 2.388 r_chiral_restr 0.188
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.225 r_dihedral_angle_4_deg 17.901 r_dihedral_angle_3_deg 15.483 r_long_range_B_refined 7.643 r_dihedral_angle_1_deg 6.287 r_mcangle_it 3.732 r_scbond_it 3.65 r_angle_refined_deg 2.455 r_mcbond_it 2.388 r_chiral_restr 0.188 r_bond_refined_d 0.025 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1975 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 33
Software Software Software Name Purpose StructureStudio data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling