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Crystal structure of TEM-1 beta-lactamase in complex with boron-based inhibitor EC25
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 6% PEG 8000, 100 mM MES buffer, 200mM Ca(OAc)2 and 50 M NaF, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.39 48.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.69 α = 90 b = 81.69 β = 90 c = 497.92 γ = 90
Symmetry Space Group P 43 21 2
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 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 2.4 45.81 96.4 0.071 14.64 5.06 65358 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 2.4 2.5 97.8 0.539 3 4.66
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 2.4 45.81 62086 3268 96.4 0.206 0.203 0.2084 0.264 0.2621 RANDOM 52.98
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] 0.32 0.32 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.269 r_dihedral_angle_4_deg 14.64 r_dihedral_angle_3_deg 13.801 r_long_range_B_refined 10.619 r_long_range_B_other 10.619 r_scangle_other 8.281 r_mcangle_it 6.84 r_mcangle_other 6.84 r_scbond_it 5.705 r_scbond_other 5.705
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.269 r_dihedral_angle_4_deg 14.64 r_dihedral_angle_3_deg 13.801 r_long_range_B_refined 10.619 r_long_range_B_other 10.619 r_scangle_other 8.281 r_mcangle_it 6.84 r_mcangle_other 6.84 r_scbond_it 5.705 r_scbond_other 5.705 r_mcbond_it 4.993 r_mcbond_other 4.99 r_dihedral_angle_1_deg 4.623 r_angle_refined_deg 0.797 r_angle_other_deg 0.516 r_chiral_restr 0.045 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 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 12180 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 126
Software Software Software Name Purpose StructureStudio data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling