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CTX-M-9 class A beta-lactamase complexed with compound 3 (G30)
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 2.08 40.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.803 α = 90 b = 41.803 β = 90 c = 230.542 γ = 120
Symmetry Space Group P 32 2 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 1.8 50 99.7 0.09 7.4 22863 -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) 1.8 1.86 98.5 0.792 5.9 2167
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 1.8 38.43 22803 1135 99.74 0.21 0.208 0.2084 0.245 0.2457 RANDOM 25.36
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] 0.97 0.48 0.97 -1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.448 r_dihedral_angle_4_deg 18.03 r_dihedral_angle_3_deg 14.164 r_dihedral_angle_1_deg 6.447 r_scangle_it 3.621 r_scbond_it 2.407 r_angle_refined_deg 1.697 r_mcangle_it 1.624 r_mcbond_it 1.091 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.448 r_dihedral_angle_4_deg 18.03 r_dihedral_angle_3_deg 14.164 r_dihedral_angle_1_deg 6.447 r_scangle_it 3.621 r_scbond_it 2.407 r_angle_refined_deg 1.697 r_mcangle_it 1.624 r_mcbond_it 1.091 r_nbtor_refined 0.302 r_nbd_refined 0.208 r_symmetry_hbond_refined 0.176 r_symmetry_vdw_refined 0.171 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.107 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1997 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 51
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