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An Ultral High Resolution Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homoserine Bound at An Alternative Site
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, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.1 41.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.929 α = 90 b = 55.604 β = 90 c = 78.703 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 of 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 0.9184 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 0.95 50 93.9 0.091 12.5 6.3 141032 15.9
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 0.95 0.98 61.9 0.371 2 2.2 9081
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R PDB entry 2A7M 0.95 45 2 150193 141032 7051 93.9 0.1327 0.1327 0.1327 0.1325 0.169 RANDOM 21.8
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 18 1951 2406.5
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.11 s_approx_iso_adps 0.11 s_zero_chiral_vol 0.098 s_similar_adp_cmpnt 0.064 s_anti_bump_dis_restr 0.058 s_angle_d 0.036 s_from_restr_planes 0.0314 s_bond_d 0.018 s_rigid_bond_adp_cmpnt 0.007 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2018 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 41
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement Blu-Ice data collection HKL-2000 data reduction SCALEPACK data scaling SHELX phasing