8C4I

Ligand-free Crystal Structure of the decameric Sulfofructose Transaldolase BmSF-TAL


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8BC2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.42980.2 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 coefficientSolvent content
2.6954.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.891α = 90
b = 120.839β = 93.401
c = 152.643γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2021-02-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.268.08499.90.1770.210.1130.9786.66.744297
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)RedundancyNumber Unique Reflections (All)
13.23.320.4980.5860.3080.9237

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3.268.08444144209599.5760.2370.23530.268246.87
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]
-1.894-0.3136.599-4.634
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.896
r_dihedral_angle_6_deg15.596
r_dihedral_angle_2_deg9.943
r_lrange_it8.751
r_lrange_other8.75
r_scangle_it6.256
r_scangle_other6.256
r_dihedral_angle_1_deg6.183
r_mcangle_it5.8
r_mcangle_other5.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.896
r_dihedral_angle_6_deg15.596
r_dihedral_angle_2_deg9.943
r_lrange_it8.751
r_lrange_other8.75
r_scangle_it6.256
r_scangle_other6.256
r_dihedral_angle_1_deg6.183
r_mcangle_it5.8
r_mcangle_other5.8
r_scbond_it3.789
r_scbond_other3.789
r_mcbond_it3.611
r_mcbond_other3.61
r_angle_refined_deg1.281
r_angle_other_deg0.472
r_nbd_refined0.249
r_symmetry_nbd_other0.205
r_nbtor_refined0.189
r_xyhbond_nbd_refined0.179
r_symmetry_xyhbond_nbd_other0.174
r_symmetry_nbd_refined0.141
r_symmetry_xyhbond_nbd_refined0.115
r_ncsr_local_group_280.108
r_nbd_other0.107
r_ncsr_local_group_220.103
r_ncsr_local_group_290.102
r_ncsr_local_group_430.099
r_ncsr_local_group_70.098
r_ncsr_local_group_270.098
r_ncsr_local_group_440.098
r_ncsr_local_group_150.097
r_ncsr_local_group_330.096
r_ncsr_local_group_400.096
r_ncsr_local_group_30.094
r_ncsr_local_group_110.094
r_ncsr_local_group_370.094
r_ncsr_local_group_410.094
r_ncsr_local_group_380.093
r_ncsr_local_group_250.09
r_ncsr_local_group_40.088
r_ncsr_local_group_180.088
r_ncsr_local_group_210.088
r_ncsr_local_group_160.087
r_ncsr_local_group_50.086
r_ncsr_local_group_300.086
r_ncsr_local_group_420.086
r_ncsr_local_group_60.085
r_ncsr_local_group_80.085
r_ncsr_local_group_130.084
r_ncsr_local_group_190.084
r_ncsr_local_group_390.084
r_ncsr_local_group_10.083
r_ncsr_local_group_20.083
r_ncsr_local_group_260.083
r_ncsr_local_group_340.083
r_ncsr_local_group_100.082
r_ncsr_local_group_140.082
r_ncsr_local_group_170.082
r_ncsr_local_group_90.081
r_ncsr_local_group_350.08
r_ncsr_local_group_230.079
r_ncsr_local_group_310.079
r_symmetry_nbtor_other0.078
r_ncsr_local_group_120.078
r_ncsr_local_group_200.078
r_ncsr_local_group_240.078
r_ncsr_local_group_320.076
r_ncsr_local_group_360.076
r_ncsr_local_group_450.074
r_chiral_restr0.069
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16741
Nucleic Acid Atoms
Solvent Atoms144
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
MOLREPphasing