6BQ6

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


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 Bis-Tris propane buffer cryo 33% PEG400
Crystal Properties
Matthews coefficientSolvent content
1.7630.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.293α = 90
b = 80.293β = 90
c = 163.245γ = 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-ID0.979APS19-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
11.6546.6199.80.06823.512.865012-3
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)
11.651.7599.11.2872.112.8

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 REPLACEMENTTHROUGHOUT6BQ21.6546.6163970104199.840.173030.172110.23027RANDOM29.913
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]
-0.12-0.120.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.598
r_dihedral_angle_4_deg26.82
r_dihedral_angle_3_deg14.674
r_dihedral_angle_1_deg6.932
r_long_range_B_refined5.524
r_long_range_B_other5.523
r_scangle_other3.102
r_mcangle_it2.403
r_mcangle_other2.403
r_scbond_it1.888
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.598
r_dihedral_angle_4_deg26.82
r_dihedral_angle_3_deg14.674
r_dihedral_angle_1_deg6.932
r_long_range_B_refined5.524
r_long_range_B_other5.523
r_scangle_other3.102
r_mcangle_it2.403
r_mcangle_other2.403
r_scbond_it1.888
r_scbond_other1.887
r_angle_refined_deg1.681
r_mcbond_it1.48
r_mcbond_other1.479
r_angle_other_deg0.997
r_chiral_restr0.105
r_bond_refined_d0.014
r_gen_planes_refined0.009
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 Atoms4663
Nucleic Acid Atoms
Solvent Atoms341
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing