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AMP-forming acetyl-CoA synthetase from Chloroflexota bacterium with bound acetyl AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 2 uL (protein in 50 mM HEPES pH 7.5, 100 mM KCl) + 2 uL (25% PEG 400, 0.1 M Na-MES, pH 6.5, 0.05 M MnCl2 or MgCl2)
Crystal Properties Matthews coefficient Solvent content 4 64.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.909 α = 90 b = 161.909 β = 90 c = 817.234 γ = 120
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 Si111 2023-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97630 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) CC (Half) 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 2.37 50 99.9 0.142 0.146 0.999 16 20.4 167479 -3 70
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.37 2.56 100 2.9 2.97 0.502 1.13 21.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.37 48.304 167354 8378 99.868 0.163 0.1613 0.1598 0.2007 0.1992 76.265
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] 0.658 0.329 0.658 -2.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.905 r_dihedral_angle_6_deg 14.338 r_dihedral_angle_2_deg 9.946 r_dihedral_angle_other_2_deg 9.47 r_lrange_it 9.01 r_lrange_other 9.01 r_scangle_it 7.511 r_scangle_other 7.511 r_dihedral_angle_1_deg 7.046 r_mcangle_it 5.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.905 r_dihedral_angle_6_deg 14.338 r_dihedral_angle_2_deg 9.946 r_dihedral_angle_other_2_deg 9.47 r_lrange_it 9.01 r_lrange_other 9.01 r_scangle_it 7.511 r_scangle_other 7.511 r_dihedral_angle_1_deg 7.046 r_mcangle_it 5.312 r_mcangle_other 5.312 r_scbond_it 5.092 r_scbond_other 5.091 r_mcbond_it 3.748 r_mcbond_other 3.745 r_angle_refined_deg 1.698 r_angle_other_deg 0.571 r_symmetry_nbd_refined 0.276 r_metal_ion_refined 0.26 r_nbd_refined 0.209 r_nbd_other 0.206 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.136 r_symmetry_xyhbond_nbd_refined 0.089 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.079 r_symmetry_xyhbond_nbd_other 0.055 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19931 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 168
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing