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Crystal Structure of Thermotoga maritima threonylcarbamoyladenosine biosynthesis complex TsaB2D2E2 bound to ATP and carboxy-AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A6A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 2 uL sample solution containing 3.1 mg/mL protein, 50 mM Tris (pH 7.5), 50 mM NaCl, 1 mM ATP and 0.1 mM MgCl2 with 2 uL reservoir solution containing 8% polyethylene glycol (PEG) 400, 100 mM KCl, 50 mM MES (pH 6.0) and 0.8 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 3.38 63.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.053 α = 90 b = 124.053 β = 90 c = 119.035 γ = 120
Symmetry Space Group P 31 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 80 CCD MARMOSAIC 325 mm CCD 2016-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 1.19499 SSRL BL14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.5 107.43 98.8 0.122 0.13 0.042 6.1 9 36821
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 2.5 2.54 84.2 1.886 2.297 1.281 0.182 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2A6A 2.5 42.94 31308 1787 89.12 0.12681 0.12185 0.1309 0.21438 0.2149 RANDOM 76.982
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] -1.66 -0.83 -1.66 5.38
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 47.744 r_sphericity_bonded 43.476 r_dihedral_angle_2_deg 33.739 r_dihedral_angle_3_deg 17.962 r_long_range_B_refined 17.051 r_long_range_B_other 17.047 r_dihedral_angle_4_deg 16.691 r_scangle_other 16.523 r_mcangle_it 13.933 r_mcangle_other 13.932
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 47.744 r_sphericity_bonded 43.476 r_dihedral_angle_2_deg 33.739 r_dihedral_angle_3_deg 17.962 r_long_range_B_refined 17.051 r_long_range_B_other 17.047 r_dihedral_angle_4_deg 16.691 r_scangle_other 16.523 r_mcangle_it 13.933 r_mcangle_other 13.932 r_scbond_it 13.315 r_scbond_other 13.305 r_mcbond_other 10.643 r_mcbond_it 10.64 r_dihedral_angle_1_deg 6.934 r_rigid_bond_restr 2.686 r_angle_refined_deg 0.783 r_angle_other_deg 0.77 r_chiral_restr 0.04 r_bond_refined_d 0.003 r_gen_planes_refined 0.001 r_bond_other_d r_gen_planes_other 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5490 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PDB_EXTRACT data extraction HKL-3000 data reduction PHENIX phasing