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AmpC beta-lactamase in complex with 2-carboxythiophene
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 1.7M potassium phosphate, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.49 50.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.434 α = 90 b = 74.781 β = 116.14 c = 98.281 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 2.1 50 91 0.089 12.8 2.5 69905
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) 2.1 2.18 78.5 0.393 2.2 2.2
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 2.1 30 41236 41236 2085 90.72 0.183 0.183 0.1877 0.227 0.1949 RANDOM 18.107
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] -0.54 0.48 -0.03 0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.029 r_dihedral_angle_4_deg 14.137 r_dihedral_angle_3_deg 13.615 r_dihedral_angle_1_deg 6.506 r_scangle_it 2.319 r_scbond_it 1.62 r_angle_refined_deg 1.526 r_angle_other_deg 0.991 r_mcangle_it 0.965 r_mcbond_it 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.029 r_dihedral_angle_4_deg 14.137 r_dihedral_angle_3_deg 13.615 r_dihedral_angle_1_deg 6.506 r_scangle_it 2.319 r_scbond_it 1.62 r_angle_refined_deg 1.526 r_angle_other_deg 0.991 r_mcangle_it 0.965 r_mcbond_it 0.86 r_symmetry_vdw_other 0.259 r_nbd_refined 0.193 r_nbd_other 0.188 r_nbtor_refined 0.176 r_symmetry_vdw_refined 0.165 r_xyhbond_nbd_refined 0.147 r_mcbond_other 0.133 r_symmetry_hbond_refined 0.11 r_nbtor_other 0.085 r_chiral_restr 0.072 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5600 Nucleic Acid Atoms Solvent Atoms 486 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction