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Crystal structure of TLA-3 extended-spectrum beta-lactamase in a complex with avibactam
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GS8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M sodium citrate, 2.8M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.36 47.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.939 α = 90 b = 68.12 β = 94.53 c = 45.33 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 CCD ADSC QUANTUM 315r 2016-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AichiSR BEAMLINE BL2S1 1.12 AichiSR BL2S1
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 1.59 55.48 98.8 0.044 28.1 7.1 38600
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.59 1.68 97.7 0.204 8.8 7
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 5GS8 1.59 55.48 36659 1941 98.65 0.16051 0.15887 0.1719 0.19169 0.2012 RANDOM 18.465
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] 0.12 -0.66 -0.17 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.436 r_dihedral_angle_3_deg 13.664 r_dihedral_angle_4_deg 7.108 r_dihedral_angle_1_deg 6.385 r_long_range_B_refined 6.155 r_long_range_B_other 6.154 r_scangle_other 4.423 r_scbond_it 3.099 r_scbond_other 3.099 r_mcangle_it 2.567
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.436 r_dihedral_angle_3_deg 13.664 r_dihedral_angle_4_deg 7.108 r_dihedral_angle_1_deg 6.385 r_long_range_B_refined 6.155 r_long_range_B_other 6.154 r_scangle_other 4.423 r_scbond_it 3.099 r_scbond_other 3.099 r_mcangle_it 2.567 r_mcangle_other 2.567 r_mcbond_it 1.947 r_mcbond_other 1.943 r_angle_refined_deg 1.47 r_angle_other_deg 0.729 r_chiral_restr 0.097 r_gen_planes_refined 0.014 r_bond_refined_d 0.011 r_gen_planes_other 0.003 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2171 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing