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AmpC beta-lactamase in complex with 5-diformylaminomethyl-benzo[b]thiophen-2-boronic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CB3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.7 294 potassium phosphate buffer, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.5 50.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.632 α = 90 b = 77.236 β = 116.73 c = 97.825 γ = 90
Symmetry Space Group C 1 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 210 2004-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.115869 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.2 45.314 98.3 0.087 0.087 7.2 3.8 39060 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.32 97.4 0.345 0.345 3.9 3.7 5590
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1CB3 2.2 45.31 39056 39056 3524 100 0.163 0.159 0.1593 0.205 0.2037 RANDOM 20.7
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] 0.77 1.15 -0.39 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.931 r_dihedral_angle_4_deg 18.3 r_dihedral_angle_3_deg 15.357 r_dihedral_angle_1_deg 6.399 r_scangle_it 4.059 r_scbond_it 2.802 r_angle_refined_deg 1.566 r_mcangle_it 1.493 r_mcbond_it 1.259 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.931 r_dihedral_angle_4_deg 18.3 r_dihedral_angle_3_deg 15.357 r_dihedral_angle_1_deg 6.399 r_scangle_it 4.059 r_scbond_it 2.802 r_angle_refined_deg 1.566 r_mcangle_it 1.493 r_mcbond_it 1.259 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.222 r_nbd_refined 0.206 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.095 r_symmetry_hbond_refined 0.094 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5476 Nucleic Acid Atoms Solvent Atoms 384 Heterogen Atoms 36
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction ELVES refinement MOSFLM data reduction CNS phasing