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CTX-M-9 class A beta-lactamase complexed with compound 11 (1CE)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YLJ PDB entry 1YLJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.7 292 Potassium Phosphate, pH 8.7, vapor diffusion, hanging drop, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2 38.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.141 α = 90 b = 106.886 β = 101.63 c = 47.445 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 Q315r mirrors 2008-06-21 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11587 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 1.31 50 99.9 0.056 3.9 106102 -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) 1.31 1.36 99.9 0.274 3.6 10591
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 1YLJ 1.31 29.22 106059 5305 99.7 0.156 0.155 0.1532 0.18 0.1788 RANDOM 13.089
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] 0.13 0.49 -0.13 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.553 r_dihedral_angle_3_deg 11.507 r_dihedral_angle_4_deg 9.619 r_dihedral_angle_1_deg 5.789 r_sphericity_free 2.333 r_scangle_it 2.131 r_sphericity_bonded 1.762 r_scbond_it 1.471 r_angle_refined_deg 1.325 r_mcangle_it 1.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.553 r_dihedral_angle_3_deg 11.507 r_dihedral_angle_4_deg 9.619 r_dihedral_angle_1_deg 5.789 r_sphericity_free 2.333 r_scangle_it 2.131 r_sphericity_bonded 1.762 r_scbond_it 1.471 r_angle_refined_deg 1.325 r_mcangle_it 1.015 r_rigid_bond_restr 0.86 r_mcbond_it 0.636 r_nbtor_refined 0.302 r_nbd_refined 0.188 r_symmetry_vdw_refined 0.152 r_symmetry_hbond_refined 0.092 r_xyhbond_nbd_refined 0.09 r_chiral_restr 0.074 r_bond_refined_d 0.006 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4051 Nucleic Acid Atoms Solvent Atoms 652 Heterogen Atoms 102
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing