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X-ray structure of the C-terminal domain (residues 366-485) of S. pombe threonylcarbamoyladenosine dehydratase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 293.15 0.2 M NaCl, 0.1 M citrate pH 5.5, 1 M (NH4)2HPO4, final pH 7.6
Crystal Properties Matthews coefficient Solvent content 2.2 44.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.45 α = 90 b = 55.49 β = 90 c = 69.39 γ = 90
Symmetry Space Group P 21 21 21
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 2020-11-08 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 1.75 43 98.1 0.072 15 4.9 12946
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 1.75 1.85 96.5 0.596 4 5.3
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION AB INITIO PHASING THROUGHOUT 1.75 30 12297 648 98.08 0.17453 0.17252 0.1871 0.21225 0.2202 RANDOM 27.629
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] -2.72 -1.14 3.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.313 r_dihedral_angle_4_deg 19.345 r_dihedral_angle_3_deg 12.452 r_dihedral_angle_1_deg 5.582 r_long_range_B_refined 3.105 r_long_range_B_other 3.02 r_scangle_other 2.353 r_mcangle_other 1.905 r_mcangle_it 1.904 r_scbond_it 1.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.313 r_dihedral_angle_4_deg 19.345 r_dihedral_angle_3_deg 12.452 r_dihedral_angle_1_deg 5.582 r_long_range_B_refined 3.105 r_long_range_B_other 3.02 r_scangle_other 2.353 r_mcangle_other 1.905 r_mcangle_it 1.904 r_scbond_it 1.83 r_scbond_other 1.771 r_mcbond_it 1.303 r_mcbond_other 1.296 r_angle_other_deg 1.191 r_angle_refined_deg 1.114 r_rigid_bond_restr 0.626 r_chiral_restr 0.052 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 991 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling Arcimboldo phasing