6BQ2

Crystal structure of Medicago truncatula Thermospermine Synthase (MtTSPS)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1INL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529210% PEG3350, 0.1 M Magnesium Chloride and 0.1 M MES buffer; cryo 33% PEG400
Crystal Properties
Matthews coefficientSolvent content
1.7931.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.53α = 90
b = 80.53β = 90
c = 164.36γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2017-03-18MSINGLE 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
11.6846.8199.70.05920.99.462270-3
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)
11.681.7898.41.05829.1

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 REPLACEMENTTHROUGHOUT1INL1.6846.8161210105999.720.176260.175570.21671RANDOM31.349
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]
-0.17-0.170.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.859
r_dihedral_angle_4_deg25.269
r_dihedral_angle_3_deg14.588
r_dihedral_angle_1_deg6.712
r_long_range_B_refined5.378
r_long_range_B_other5.378
r_scangle_other2.945
r_mcangle_it2.134
r_mcangle_other2.134
r_scbond_it1.778
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.859
r_dihedral_angle_4_deg25.269
r_dihedral_angle_3_deg14.588
r_dihedral_angle_1_deg6.712
r_long_range_B_refined5.378
r_long_range_B_other5.378
r_scangle_other2.945
r_mcangle_it2.134
r_mcangle_other2.134
r_scbond_it1.778
r_scbond_other1.777
r_angle_refined_deg1.634
r_mcbond_it1.293
r_mcbond_other1.292
r_angle_other_deg1.284
r_chiral_restr0.104
r_bond_refined_d0.013
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 Atoms4651
Nucleic Acid Atoms
Solvent Atoms302
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing