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Ligand-free Crystal Structure of the decameric Sulfofructose Transaldolase BmSF-TAL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BC2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 298 0.2 M NaSO4, 0.1 M bis-TRIS propane, 20% PEG 3350, with a 3:2 protein:mother liquor ratio and 1 ul drop size.
Protein was used in 50 mM TRIS, 300 mM NaCl pH 7.4 at 23 mg/ml
Crystal Properties Matthews coefficient Solvent content 2.69 54.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.891 α = 90 b = 120.839 β = 93.401 c = 152.643 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M-F 2021-02-03 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) R Merge I (Observed) Rrim I (All) Rpim 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 3.2 68.084 99.9 0.177 0.21 0.113 0.978 6.6 6.7 44297
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 3.2 3.32 0.498 0.586 0.308 0.923 7
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 3.2 68.084 44144 2095 99.576 0.237 0.2353 0.234 0.2682 0.2611 46.87
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] -1.894 -0.313 6.599 -4.634
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.896 r_dihedral_angle_6_deg 15.596 r_dihedral_angle_2_deg 9.943 r_lrange_it 8.751 r_lrange_other 8.75 r_scangle_it 6.256 r_scangle_other 6.256 r_dihedral_angle_1_deg 6.183 r_mcangle_it 5.8 r_mcangle_other 5.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.896 r_dihedral_angle_6_deg 15.596 r_dihedral_angle_2_deg 9.943 r_lrange_it 8.751 r_lrange_other 8.75 r_scangle_it 6.256 r_scangle_other 6.256 r_dihedral_angle_1_deg 6.183 r_mcangle_it 5.8 r_mcangle_other 5.8 r_scbond_it 3.789 r_scbond_other 3.789 r_mcbond_it 3.611 r_mcbond_other 3.61 r_angle_refined_deg 1.281 r_angle_other_deg 0.472 r_nbd_refined 0.249 r_symmetry_nbd_other 0.205 r_nbtor_refined 0.189 r_xyhbond_nbd_refined 0.179 r_symmetry_xyhbond_nbd_other 0.174 r_symmetry_nbd_refined 0.141 r_symmetry_xyhbond_nbd_refined 0.115 r_ncsr_local_group_28 0.108 r_nbd_other 0.107 r_ncsr_local_group_22 0.103 r_ncsr_local_group_29 0.102 r_ncsr_local_group_43 0.099 r_ncsr_local_group_7 0.098 r_ncsr_local_group_27 0.098 r_ncsr_local_group_44 0.098 r_ncsr_local_group_15 0.097 r_ncsr_local_group_33 0.096 r_ncsr_local_group_40 0.096 r_ncsr_local_group_3 0.094 r_ncsr_local_group_11 0.094 r_ncsr_local_group_37 0.094 r_ncsr_local_group_41 0.094 r_ncsr_local_group_38 0.093 r_ncsr_local_group_25 0.09 r_ncsr_local_group_4 0.088 r_ncsr_local_group_18 0.088 r_ncsr_local_group_21 0.088 r_ncsr_local_group_16 0.087 r_ncsr_local_group_5 0.086 r_ncsr_local_group_30 0.086 r_ncsr_local_group_42 0.086 r_ncsr_local_group_6 0.085 r_ncsr_local_group_8 0.085 r_ncsr_local_group_13 0.084 r_ncsr_local_group_19 0.084 r_ncsr_local_group_39 0.084 r_ncsr_local_group_1 0.083 r_ncsr_local_group_2 0.083 r_ncsr_local_group_26 0.083 r_ncsr_local_group_34 0.083 r_ncsr_local_group_10 0.082 r_ncsr_local_group_14 0.082 r_ncsr_local_group_17 0.082 r_ncsr_local_group_9 0.081 r_ncsr_local_group_35 0.08 r_ncsr_local_group_23 0.079 r_ncsr_local_group_31 0.079 r_symmetry_nbtor_other 0.078 r_ncsr_local_group_12 0.078 r_ncsr_local_group_20 0.078 r_ncsr_local_group_24 0.078 r_ncsr_local_group_32 0.076 r_ncsr_local_group_36 0.076 r_ncsr_local_group_45 0.074 r_chiral_restr 0.069 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16741 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling MOLREP phasing