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Crystal structure of TLA-3 extended-spectrum beta-lactamase in a complex with OP0595
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 2.33 47.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.19 α = 90 b = 67.91 β = 94.6 c = 45.32 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 2015-12-11 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 2 55.22 97 0.074 20 7.5 18894
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 2 2.11 95.6 0.295 6.6 7.6 2688
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 2 55.22 17989 903 96.7 0.16313 0.16065 0.1712 0.2086 0.2153 RANDOM 20.633
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] -0.16 -0.97 -0.85 1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.856 r_dihedral_angle_3_deg 15.491 r_dihedral_angle_4_deg 13.13 r_dihedral_angle_1_deg 6.953 r_long_range_B_refined 5.955 r_long_range_B_other 5.955 r_scangle_other 4.903 r_scbond_it 3.546 r_scbond_other 3.545 r_mcangle_it 2.915
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.856 r_dihedral_angle_3_deg 15.491 r_dihedral_angle_4_deg 13.13 r_dihedral_angle_1_deg 6.953 r_long_range_B_refined 5.955 r_long_range_B_other 5.955 r_scangle_other 4.903 r_scbond_it 3.546 r_scbond_other 3.545 r_mcangle_it 2.915 r_mcangle_other 2.914 r_mcbond_it 2.247 r_mcbond_other 2.226 r_angle_refined_deg 1.477 r_angle_other_deg 0.775 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.013 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 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 172 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing