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Crystal Structure of the Mobile Metallo-beta-Lactamase AIM-1 from Pseudomonas aeruginosa: Insights into Antibiotic Binding and the role of Gln157
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 19% POLYETHYLENE GLYCOL MONOMETHYL ETHERS (PEG MME) 2000, 0.1 M CALCIUM ACETATE AND 0.1M SODIUM CACODYLATE AT PH 5.0
Crystal Properties Matthews coefficient Solvent content 3.27 62.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.831 α = 90 b = 77.831 β = 90 c = 239.018 γ = 120
Symmetry Space Group P 61 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 CCD ADSC QUANTUM 315r 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 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 1.6 28 97.8 0.05 5.5 56470 14.57
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 1.6 1.68 87 0.14 6.6 3.9
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 1SML 1.6 20 53538 2857 97.7 0.13037 0.12893 0.1417 0.15805 0.1674 RANDOM 11.661
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] -0.04 -0.02 -0.04 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.036 r_dihedral_angle_4_deg 21.374 r_dihedral_angle_3_deg 12.61 r_dihedral_angle_1_deg 6.412 r_scangle_it 5.475 r_scbond_it 3.808 r_mcangle_it 2.47 r_angle_refined_deg 1.619 r_mcbond_it 1.611 r_rigid_bond_restr 1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.036 r_dihedral_angle_4_deg 21.374 r_dihedral_angle_3_deg 12.61 r_dihedral_angle_1_deg 6.412 r_scangle_it 5.475 r_scbond_it 3.808 r_mcangle_it 2.47 r_angle_refined_deg 1.619 r_mcbond_it 1.611 r_rigid_bond_restr 1.52 r_angle_other_deg 1.029 r_mcbond_other 0.556 r_chiral_restr 0.104 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.005 r_gen_planes_other 0.002 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2005 Nucleic Acid Atoms Solvent Atoms 385 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing