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Structure of the Quorum Quenching lactonase from Alicyclobacillus acidoterrestris bound to a phosphate anion
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 292 Purified and concentrated AaL samples (10 mg ml) were subjected to crystallization trialsCrystals appeared after 1 d at 292 K in a condition consisting of 0.45M ammonium chloride, 16% polyethylene glycol 3350. Seeding was performed as described previously (PMID: 28777091)
Crystal Properties Matthews coefficient Solvent content 2.51 50.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.72 α = 90 b = 114.74 β = 109.78 c = 79.97 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 PIXEL DECTRIS EIGER X 16M 2017-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033200 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.65 19.9 98.2 0.036 22.08 3.86 111796
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.75 97.2 0.591 3.16 3.94
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 1.65 19.9 106205 5590 98.33 0.17172 0.17039 0.1806 0.19737 0.2049 RANDOM 27.88
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] 0.03 -0.06 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.694 r_dihedral_angle_4_deg 16.854 r_dihedral_angle_3_deg 12.271 r_long_range_B_refined 6.765 r_long_range_B_other 6.764 r_scangle_other 6.005 r_dihedral_angle_1_deg 5.323 r_scbond_it 4.339 r_scbond_other 4.16 r_mcangle_other 3.498
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.694 r_dihedral_angle_4_deg 16.854 r_dihedral_angle_3_deg 12.271 r_long_range_B_refined 6.765 r_long_range_B_other 6.764 r_scangle_other 6.005 r_dihedral_angle_1_deg 5.323 r_scbond_it 4.339 r_scbond_other 4.16 r_mcangle_other 3.498 r_mcangle_it 3.496 r_mcbond_it 2.722 r_mcbond_other 2.713 r_angle_refined_deg 1.164 r_angle_other_deg 0.644 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6631 Nucleic Acid Atoms Solvent Atoms 414 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing