8K57

Crystal structure of sulfur transferase from Frondihabitans sp. PAMC28461 crystallized in the I21 space group


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherwildtype

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29410% w/v PEG 20,000, 20% v/v PEG MME 550, 0.03 M of magnesium chloride and calcium chloride as divalent cations, and 0.1 M MOPS/HEPES-Na pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.0339.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.47α = 90
b = 34.76β = 105.722
c = 93.365γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2021-07-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 5C (4A)0.9794PAL/PLS5C (4A)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.3829.14799.30.998.43.711072
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.382.470.84

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-VALUE2.3829.1471107163199.1670.1840.180.261335.072
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]
0.010.0350.035-0.056
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.739
r_dihedral_angle_4_deg17.123
r_dihedral_angle_3_deg15.955
r_dihedral_angle_1_deg7.748
r_lrange_it7.047
r_lrange_other7.047
r_scangle_it5.203
r_scangle_other5.202
r_mcangle_it4.471
r_mcangle_other4.469
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.739
r_dihedral_angle_4_deg17.123
r_dihedral_angle_3_deg15.955
r_dihedral_angle_1_deg7.748
r_lrange_it7.047
r_lrange_other7.047
r_scangle_it5.203
r_scangle_other5.202
r_mcangle_it4.471
r_mcangle_other4.469
r_scbond_it3.45
r_scbond_other3.449
r_mcbond_it3.034
r_mcbond_other3.034
r_angle_refined_deg1.579
r_angle_other_deg1.268
r_symmetry_nbd_refined0.319
r_symmetry_xyhbond_nbd_refined0.236
r_nbd_refined0.208
r_nbd_other0.206
r_symmetry_nbd_other0.187
r_nbtor_refined0.168
r_xyhbond_nbd_refined0.155
r_symmetry_nbtor_other0.078
r_chiral_restr0.066
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2325
Nucleic Acid Atoms
Solvent Atoms36
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MERLOTphasing