☰ Navigation Tabs
1.3 Angstrom Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homocysteine Bound to 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, MgCl2, N-Hexanoyl-L-Homocysteine Thiolactone, Methanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.1 41.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.775 α = 90 b = 55.46 β = 90 c = 79.191 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 1.3 50 94.4 0.051 14.5 6.6 60162 56793 22.4
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 1.3 1.35 67.5 0.481 2.1 3.8
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 2A7M 1.3 23.62 60162 53865 2869 94.4 0.145 0.143 0.1386 0.183 0.1787 RANDOM 22.4
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] -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.452 r_dihedral_angle_4_deg 21.579 r_dihedral_angle_3_deg 12.242 r_scangle_it 6.622 r_dihedral_angle_1_deg 6.49 r_scbond_it 4.965 r_mcangle_it 3.331 r_mcbond_it 2.465 r_angle_refined_deg 2.05 r_nbtor_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.452 r_dihedral_angle_4_deg 21.579 r_dihedral_angle_3_deg 12.242 r_scangle_it 6.622 r_dihedral_angle_1_deg 6.49 r_scbond_it 4.965 r_mcangle_it 3.331 r_mcbond_it 2.465 r_angle_refined_deg 2.05 r_nbtor_refined 0.322 r_chiral_restr 0.267 r_xyhbond_nbd_refined 0.217 r_nbd_refined 0.216 r_symmetry_vdw_refined 0.186 r_symmetry_hbond_refined 0.148 r_metal_ion_refined 0.054 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1989 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing