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AMP-forming Acetyl-CoA synthetase from Chloroflexota bacterium without bound ligand
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 3.43 64.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.352 α = 90 b = 161.352 β = 90 c = 814.182 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 mirror 2023-09-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.615 272 81.5 0.119 0.122 0.027 0.999 19.1 2.6 100973 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.62 2.82 20.4 1.952 2.002 0.445 0.711 1.7 20
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 FREE R-VALUE 2.615 272 100973 5010 81.507 0.166 0.1629 0.1635 0.2213 0.222 78.727
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] -0.376 -0.188 -0.376 1.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.936 r_dihedral_angle_6_deg 14.535 r_dihedral_angle_2_deg 10.832 r_lrange_it 9.127 r_lrange_other 9.127 r_scangle_it 7.903 r_scangle_other 7.903 r_dihedral_angle_1_deg 7.689 r_mcangle_it 6.459 r_mcangle_other 6.459
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.936 r_dihedral_angle_6_deg 14.535 r_dihedral_angle_2_deg 10.832 r_lrange_it 9.127 r_lrange_other 9.127 r_scangle_it 7.903 r_scangle_other 7.903 r_dihedral_angle_1_deg 7.689 r_mcangle_it 6.459 r_mcangle_other 6.459 r_scbond_it 5.503 r_scbond_other 5.502 r_mcbond_it 4.613 r_mcbond_other 4.613 r_angle_refined_deg 1.872 r_angle_other_deg 0.615 r_symmetry_nbd_refined 0.252 r_nbd_refined 0.216 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.188 r_nbd_other 0.178 r_xyhbond_nbd_refined 0.139 r_symmetry_xyhbond_nbd_refined 0.096 r_metal_ion_refined 0.088 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.082 r_symmetry_xyhbond_nbd_other 0.046 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19896 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing