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1.4 Angstrom Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homoserine Bound at The Catalytic Metal Center
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A7M PDB entry 2A7M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 Glycerol, Tris-HCl, PEG4000, MgCl2, N-Hexanoyl-L-homoserine lactone, Methanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.15 42.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.438 α = 90 b = 55.583 β = 90 c = 79.866 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 300 mm CCD K-B pair biomorph mirrors 2006-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97934 APS 23-ID-D
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 1.4 45.64 97 0.053 14 6.9 49268 20.5
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 1.4 1.45 90.6 0.512 2.4 4.7 4408
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2A7M 1.4 18.79 2.4 47158 45744 2446 97.76 0.144 0.144 0.14189 0.1371 0.18409 0.1809 RANDOM 20.668
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] 0.2 0.35 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.968 r_dihedral_angle_4_deg 22.045 r_dihedral_angle_3_deg 11.767 r_dihedral_angle_1_deg 6.076 r_scangle_it 4.976 r_scbond_it 3.643 r_mcangle_it 2.273 r_angle_refined_deg 1.619 r_mcbond_it 1.541 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.968 r_dihedral_angle_4_deg 22.045 r_dihedral_angle_3_deg 11.767 r_dihedral_angle_1_deg 6.076 r_scangle_it 4.976 r_scbond_it 3.643 r_mcangle_it 2.273 r_angle_refined_deg 1.619 r_mcbond_it 1.541 r_nbtor_refined 0.316 r_symmetry_vdw_refined 0.239 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.111 r_symmetry_hbond_refined 0.097 r_metal_ion_refined 0.034 r_bond_refined_d 0.013 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1989 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing