6CD1

Crystal structure of Medicago truncatula serine hydroxymethyltransferase 3 (MtSHMT3), complexes with reaction intermediates


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529275 mM MES pH 6.5, 19% PEG3350 and 150 mM ammonium acetate. The mature crystals were soaked with 200 mM Ser for 2 h and cryoprotected by the addition of ethylene glycol to a final concentration of 20%
Crystal Properties
Matthews coefficientSolvent content
2.1943.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.086α = 90
b = 103.653β = 97.38
c = 180.379γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9792APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.915098.60.0630.07113.34.7263165
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.912.0297.30.730.831.94.7

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 REPLACEMENTTHROUGHOUT6ccz1.9146.65261832131698.60.1910.1910.236RANDOM40.906
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]
-0.770.431.24-0.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.369
r_dihedral_angle_3_deg14.302
r_dihedral_angle_4_deg13.195
r_dihedral_angle_1_deg6.432
r_long_range_B_refined5.185
r_long_range_B_other5.185
r_scangle_other2.227
r_mcangle_it1.886
r_mcangle_other1.886
r_angle_refined_deg1.529
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.369
r_dihedral_angle_3_deg14.302
r_dihedral_angle_4_deg13.195
r_dihedral_angle_1_deg6.432
r_long_range_B_refined5.185
r_long_range_B_other5.185
r_scangle_other2.227
r_mcangle_it1.886
r_mcangle_other1.886
r_angle_refined_deg1.529
r_scbond_it1.322
r_scbond_other1.322
r_mcbond_it1.163
r_mcbond_other1.163
r_angle_other_deg0.98
r_chiral_restr0.087
r_bond_refined_d0.012
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 Atoms27693
Nucleic Acid Atoms
Solvent Atoms2032
Heterogen Atoms138

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing