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AmpC beta-lactamase in complex with 4-Amino-3-hydroxybenzoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KE4 PDB ENTRY 1KE4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.7 294 1.8M potassium phosphate, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.49 50.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.239 α = 90 b = 77.34 β = 118.44 c = 99.01 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 2005-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1 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 2.2 50 97.5 0.076 8.1 3.1 38774 38774
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) 2.2 2.28 97 0.416 2.5 3829
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 (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 1KE4 2.2 30 38763 38763 1941 97.45 0.197 0.197 0.2001 0.246 0.2491 RANDOM 21.22
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] 0.31 0.54 0.06 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.197 r_dihedral_angle_3_deg 12.168 r_dihedral_angle_4_deg 11.856 r_dihedral_angle_1_deg 5.389 r_scangle_it 1.752 r_scbond_it 1.147 r_angle_refined_deg 1.022 r_angle_other_deg 0.811 r_mcangle_it 0.793 r_mcbond_it 0.709
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.197 r_dihedral_angle_3_deg 12.168 r_dihedral_angle_4_deg 11.856 r_dihedral_angle_1_deg 5.389 r_scangle_it 1.752 r_scbond_it 1.147 r_angle_refined_deg 1.022 r_angle_other_deg 0.811 r_mcangle_it 0.793 r_mcbond_it 0.709 r_symmetry_vdw_other 0.228 r_nbd_refined 0.182 r_nbtor_refined 0.176 r_nbd_other 0.173 r_symmetry_hbond_refined 0.16 r_xyhbond_nbd_refined 0.124 r_mcbond_other 0.092 r_symmetry_vdw_refined 0.09 r_nbtor_other 0.081 r_chiral_restr 0.057 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5557 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 170
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction