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X-ray crystallographic structure of CTX-M-9 beta-lactamase complexed with a boronic acid inhibitor (SM2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YLJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.8 293 potassium phosphate, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 8.80
Crystal Properties Matthews coefficient Solvent content 1.69 27.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.12 α = 90 b = 106.717 β = 101.89 c = 47.718 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 100 CCD ADSC QUANTUM 4 MIRRORS 2004-07-17 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) 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 1.12 30 85.1 0.054 22.9 9.01 143714 -3
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) 1.12 1.16 23.1 0.287 1.92
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 (All) 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 FREE R 1YLJ 1.12 10 133427 133427 6644 79.1 0.106 0.107 0.107 0.1191 0.14 0.1468 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 86 3767.81 4732.8
RMS Deviations Key Refinement Restraint Deviation s_zero_chiral_vol 0.103 s_approx_iso_adps 0.074 s_non_zero_chiral_vol 0.058 s_from_restr_planes 0.037 s_similar_adp_cmpnt 0.026 s_angle_d 0.022 s_anti_bump_dis_restr 0.017 s_bond_d 0.006 s_rigid_bond_adp_cmpnt 0.001 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4211 Nucleic Acid Atoms Solvent Atoms 861 Heterogen Atoms 64
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement DENZO data reduction SCALEPACK data scaling SHELX phasing