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CTX-M-9 in complex with the broad spectrum inhibitor 3-(2- carboxyvinyl)benzo(b)thiophene-2-boronic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YM1 pdb entry 1YM1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.8 295 1.4 M potassium phosphate buffer using microseeding techniques, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 8.8
Crystal Properties Matthews coefficient Solvent content 2 38.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.116 α = 90 b = 106.595 β = 102.03 c = 47.68 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 210 Mirrors 2004-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.35 20 85.9 82707 82595 -3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1YM1 1.5 19.39 82707 65055 3455 97.48 0.16048 0.15935 0.1587 0.18174 0.18 RANDOM 10.214
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.085 r_dihedral_angle_3_deg 11.686 r_dihedral_angle_4_deg 8.006 r_dihedral_angle_1_deg 5.816 r_angle_refined_deg 1.313 r_mcangle_it 0.753 r_scbond_it 0.448 r_mcbond_it 0.414 r_chiral_restr 0.085 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.085 r_dihedral_angle_3_deg 11.686 r_dihedral_angle_4_deg 8.006 r_dihedral_angle_1_deg 5.816 r_angle_refined_deg 1.313 r_mcangle_it 0.753 r_scbond_it 0.448 r_mcbond_it 0.414 r_chiral_restr 0.085 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3907 Nucleic Acid Atoms Solvent Atoms 774 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement CNS refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing HKL-2000 data collection