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X-ray structure of S. cerevisiae threonylcarbamoyladenosine dehydratase 1 (residues 50-429) in complex with 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, SITTING DROP 7 293.15 1.98 M sodium malonate pH 7.0
Crystal Properties Matthews coefficient Solvent content 6.59 81.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 259.44 α = 90 b = 259.44 β = 90 c = 236.11 γ = 120
Symmetry Space Group P 65 2 2
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 2022-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 4 49 98.8 0.171 8.1 5.7 39562
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 4 4.1 99.7 0.812 2.33 5.9
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 4 30 37500 1974 98.54 0.25686 0.25462 0.2489 0.29921 0.29 RANDOM 114.14
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] -0.53 -0.27 -0.53 1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.346 r_dihedral_angle_3_deg 17.331 r_dihedral_angle_4_deg 12.726 r_long_range_B_refined 8.412 r_long_range_B_other 8.412 r_dihedral_angle_1_deg 6.683 r_mcangle_it 4.963 r_mcangle_other 4.963 r_scangle_other 3.903 r_mcbond_it 2.748
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.346 r_dihedral_angle_3_deg 17.331 r_dihedral_angle_4_deg 12.726 r_long_range_B_refined 8.412 r_long_range_B_other 8.412 r_dihedral_angle_1_deg 6.683 r_mcangle_it 4.963 r_mcangle_other 4.963 r_scangle_other 3.903 r_mcbond_it 2.748 r_mcbond_other 2.748 r_scbond_it 2.034 r_scbond_other 2.034 r_angle_refined_deg 1.234 r_angle_other_deg 1.059 r_chiral_restr 0.043 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 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 11593 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 111
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing