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Crystal structure of Thermus thermophilus HB8 transaldolase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S1V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.26 M (NH4)SO4, 0.2 M LiSO4, 0.1 M Tris-HCl pH8.5
Crystal Properties Matthews coefficient Solvent content 3.5 64.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.38 α = 90 b = 173.38 β = 90 c = 422.58 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 PILATUS3 6M 2025-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 49.75 99.7 0.12 0.997 17.4 20 402504
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 100 0.89 2.4
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 3S1V 1.7 49.75 382265 20239 99.27 0.19051 0.18942 0.1983 0.21109 0.2163 RANDOM 30.653
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] 0.13 0.07 0.13 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.729 r_dihedral_angle_2_deg 9.893 r_long_range_B_refined 8.605 r_long_range_B_other 8.573 r_scangle_other 7.368 r_dihedral_angle_1_deg 7 r_scbond_it 5.39 r_scbond_other 5.39 r_mcangle_it 4.345 r_mcangle_other 4.345
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.729 r_dihedral_angle_2_deg 9.893 r_long_range_B_refined 8.605 r_long_range_B_other 8.573 r_scangle_other 7.368 r_dihedral_angle_1_deg 7 r_scbond_it 5.39 r_scbond_other 5.39 r_mcangle_it 4.345 r_mcangle_other 4.345 r_mcbond_it 3.373 r_mcbond_other 3.373 r_angle_refined_deg 0.693 r_angle_other_deg 0.25 r_chiral_restr 0.035 r_bond_refined_d 0.001 r_gen_planes_refined 0.001 r_bond_other_d r_dihedral_angle_4_deg 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17050 Nucleic Acid Atoms Solvent Atoms 1482 Heterogen Atoms 203
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing