6BQ3

Crystal structure of Medicago truncatula Thermospermine Synthase (MtTSPS) in complex with 5'-S-(3-aminopropyl)-5'-thioadenosine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6BQ2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529210% PEG3350, 0.1 M Magnesium Chloride, 0.1 M MES buffer; cryo 33% PEG400, 10% PEG3350, 0.1 M Magnesium Chloride, Bis-Tris propane pH 6.5
Crystal Properties
Matthews coefficientSolvent content
1.831.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.052α = 90
b = 81.052β = 90
c = 163.128γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2017-08-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.9172.5999.90.07517.45.643034-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9121000.7412.15.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6BQ21.9172.5941900106099.840.190340.189130.23793RANDOM41.683
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]
-0.09-0.090.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.656
r_dihedral_angle_4_deg26.114
r_dihedral_angle_3_deg15.156
r_dihedral_angle_1_deg6.954
r_long_range_B_refined4.192
r_long_range_B_other4.192
r_scangle_other2.216
r_mcangle_it1.861
r_mcangle_other1.861
r_angle_refined_deg1.614
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.656
r_dihedral_angle_4_deg26.114
r_dihedral_angle_3_deg15.156
r_dihedral_angle_1_deg6.954
r_long_range_B_refined4.192
r_long_range_B_other4.192
r_scangle_other2.216
r_mcangle_it1.861
r_mcangle_other1.861
r_angle_refined_deg1.614
r_scbond_it1.399
r_scbond_other1.399
r_mcbond_it1.217
r_mcbond_other1.217
r_angle_other_deg0.988
r_chiral_restr0.1
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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 AtomsNumber
Protein Atoms4672
Nucleic Acid Atoms
Solvent Atoms163
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing