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CTX-M-9 class A beta-lactamase complexed with compound 2 (GZ2)
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 2.02 39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.211 α = 90 b = 107.256 β = 101.68 c = 47.512 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 2008-07-28 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 1.5 50 98.3 0.057 2.5 69225 -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) 1.5 1.55 93.5 0.41 2 6567
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1YLJ 1.5 44.28 69190 3490 97.83 0.153 0.151 0.188 0.2035 RANDOM 18.717
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] -0.05 0.75 -0.47 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.715 r_dihedral_angle_4_deg 12.468 r_dihedral_angle_3_deg 12.242 r_dihedral_angle_1_deg 5.637 r_sphericity_free 2.927 r_scangle_it 2.772 r_scbond_it 2.288 r_sphericity_bonded 1.862 r_rigid_bond_restr 1.842 r_angle_refined_deg 1.277
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.715 r_dihedral_angle_4_deg 12.468 r_dihedral_angle_3_deg 12.242 r_dihedral_angle_1_deg 5.637 r_sphericity_free 2.927 r_scangle_it 2.772 r_scbond_it 2.288 r_sphericity_bonded 1.862 r_rigid_bond_restr 1.842 r_angle_refined_deg 1.277 r_mcangle_it 1.149 r_mcbond_it 0.749 r_nbtor_refined 0.302 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.132 r_symmetry_hbond_refined 0.124 r_xyhbond_nbd_refined 0.116 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3989 Nucleic Acid Atoms Solvent Atoms 576 Heterogen Atoms 54
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