6BQ4

Crystal structure of Medicago truncatula Thermospermine Synthase (MtTSPS) in complex with adenosine


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: 25% glycerol, Bis-Tris propane pH 6.5, 10% PEG3350, 0.1 M Magnesium Chloride
Crystal Properties
Matthews coefficientSolvent content
1.8232.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.04α = 90
b = 81.04β = 90
c = 163.8γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-04-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9793APS19-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
11.8946.9599.80.06723.912.844135-3
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)
11.892.0198.91.2682.413

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 REPLACEMENTTHROUGHOUT6BQ21.8946.9543117101699.780.187970.186860.23546RANDOM43.123
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]
-0.08-0.080.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.664
r_dihedral_angle_4_deg22.704
r_dihedral_angle_3_deg14.958
r_dihedral_angle_1_deg7.155
r_long_range_B_refined5.701
r_long_range_B_other5.7
r_scangle_other3.572
r_mcangle_it2.755
r_mcangle_other2.754
r_scbond_it2.278
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.664
r_dihedral_angle_4_deg22.704
r_dihedral_angle_3_deg14.958
r_dihedral_angle_1_deg7.155
r_long_range_B_refined5.701
r_long_range_B_other5.7
r_scangle_other3.572
r_mcangle_it2.755
r_mcangle_other2.754
r_scbond_it2.278
r_scbond_other2.278
r_mcbond_it1.798
r_mcbond_other1.798
r_angle_refined_deg1.793
r_angle_other_deg1.025
r_chiral_restr0.102
r_bond_refined_d0.016
r_gen_planes_refined0.008
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 Atoms180
Heterogen Atoms81

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing