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Crystal structure of sulfoacetaldehyde acetyltransferase in complex with ATP and inactive cofactor 3-deaza-ThDP
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, SITTING DROP 293 20 % w/v PEG 3350, 0.2 M Potassium thiocyanate 0.1 M Bis-Tris propane 7.5, 5 mM 3-deazathiamin diphosphate, 5 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.45 49.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 360.076 α = 90 b = 81.588 β = 90.562 c = 174.824 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 EIGER2 XE 16M 2022-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.85 174.82 88.1 0.11 1 11.9 6.9 282644
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 2.06 65.2 1.108 0.7 1.8 7.3
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 1.854 174.816 282644 14243 65.856 0.172 0.1704 0.1704 0.2023 0.2023 29.876
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] -0.25 0.188 -0.041 0.288
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.344 r_dihedral_angle_3_deg 11.52 r_dihedral_angle_2_deg 6.798 r_dihedral_angle_1_deg 6.326 r_lrange_it 5.525 r_scangle_it 3.236 r_scbond_it 2.168 r_mcangle_it 2.038 r_angle_refined_deg 1.611 r_mcbond_it 1.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.344 r_dihedral_angle_3_deg 11.52 r_dihedral_angle_2_deg 6.798 r_dihedral_angle_1_deg 6.326 r_lrange_it 5.525 r_scangle_it 3.236 r_scbond_it 2.168 r_mcangle_it 2.038 r_angle_refined_deg 1.611 r_mcbond_it 1.323 r_nbtor_refined 0.308 r_symmetry_xyhbond_nbd_refined 0.207 r_nbd_refined 0.199 r_symmetry_nbd_refined 0.185 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.102 r_ncsr_local_group_1 0.041 r_ncsr_local_group_7 0.04 r_ncsr_local_group_10 0.04 r_ncsr_local_group_3 0.039 r_ncsr_local_group_19 0.039 r_ncsr_local_group_23 0.039 r_ncsr_local_group_25 0.039 r_ncsr_local_group_26 0.039 r_ncsr_local_group_5 0.038 r_ncsr_local_group_12 0.038 r_ncsr_local_group_16 0.038 r_ncsr_local_group_21 0.037 r_ncsr_local_group_8 0.036 r_ncsr_local_group_14 0.036 r_ncsr_local_group_28 0.036 r_ncsr_local_group_27 0.034 r_ncsr_local_group_18 0.033 r_ncsr_local_group_11 0.031 r_ncsr_local_group_15 0.03 r_ncsr_local_group_20 0.03 r_ncsr_local_group_17 0.027 r_ncsr_local_group_2 0.026 r_ncsr_local_group_9 0.026 r_ncsr_local_group_24 0.026 r_ncsr_local_group_13 0.024 r_ncsr_local_group_4 0.023 r_ncsr_local_group_6 0.023 r_ncsr_local_group_22 0.022 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 36420 Nucleic Acid Atoms Solvent Atoms 2683 Heterogen Atoms 472
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing