6CD0

Crystal structure of Medicago truncatula serine hydroxymethyltransferase 3 (MtSHMT3), PLP-internal aldimine and apo form


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729255% Tacsimate pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.550.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 151.657α = 90
b = 201.563β = 90
c = 64.782γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2017-11-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.000APS22-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
11.749099.60.0560.06316.74.5203236
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)
11.741.8498.50.931.061.94.3

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 REPLACEMENTTHROUGHOUT6CCZ1.7483.94202206101799.60.1750.1750.219RANDOM33.125
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]
0.81-1.710.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.988
r_dihedral_angle_4_deg15.666
r_dihedral_angle_3_deg13.002
r_long_range_B_refined6.442
r_long_range_B_other6.441
r_dihedral_angle_1_deg6.323
r_scangle_other1.749
r_mcangle_it1.529
r_mcangle_other1.529
r_angle_refined_deg1.427
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.988
r_dihedral_angle_4_deg15.666
r_dihedral_angle_3_deg13.002
r_long_range_B_refined6.442
r_long_range_B_other6.441
r_dihedral_angle_1_deg6.323
r_scangle_other1.749
r_mcangle_it1.529
r_mcangle_other1.529
r_angle_refined_deg1.427
r_scbond_it1.029
r_scbond_other1.029
r_angle_other_deg0.954
r_mcbond_it0.87
r_mcbond_other0.868
r_chiral_restr0.084
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_gen_planes_other0.003
r_bond_other_d0.002
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 Atoms13917
Nucleic Acid Atoms
Solvent Atoms1409
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing