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Structural Basis for the Broad-Spectrum Inhibition of Metallo-{Beta}-Lactamases: L1- IS38 Complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SML PDB ENTRY 1SML
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 280 PEG, AS, PH 6.50, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 100K, temperature 280K
Crystal Properties Matthews coefficient Solvent content 2.5 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.319 α = 90 b = 105.319 β = 90 c = 97.96 γ = 120
Symmetry Space Group P 64 2 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 IMAGE PLATE MARRESEARCH 2006-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OTHER 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.86 50 96.5 0.084 0.084 28.1 13.7 22311 21311 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 94.2 0.404 0.404 5.5 11
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 PDB ENTRY 1SML 2 26.54 2 2 22311 20217 1092 95.94 0.17106 0.16988 0.1797 0.19249 0.2021 RANDOM 30.524
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] 0.56 0.28 0.56 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.247 r_dihedral_angle_3_deg 14.425 r_dihedral_angle_4_deg 13.73 r_dihedral_angle_1_deg 6.069 r_scangle_it 2.805 r_scbond_it 1.875 r_angle_refined_deg 1.406 r_mcangle_it 1.17 r_mcbond_it 1.035 r_angle_other_deg 0.929
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.247 r_dihedral_angle_3_deg 14.425 r_dihedral_angle_4_deg 13.73 r_dihedral_angle_1_deg 6.069 r_scangle_it 2.805 r_scbond_it 1.875 r_angle_refined_deg 1.406 r_mcangle_it 1.17 r_mcbond_it 1.035 r_angle_other_deg 0.929 r_symmetry_vdw_other 0.292 r_nbd_refined 0.203 r_nbd_other 0.195 r_nbtor_refined 0.174 r_mcbond_other 0.165 r_xyhbond_nbd_refined 0.153 r_symmetry_hbond_refined 0.15 r_nbtor_other 0.087 r_chiral_restr 0.08 r_symmetry_vdw_refined 0.069 r_metal_ion_refined 0.033 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2001 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 29
Software Software Software Name Purpose CCP4 model building REFMAC refinement MAR345dtb data collection MOSFLM data reduction SCALA data scaling CCP4 phasing