6SK4

Methyltransferase MtgA from Desulfitobacterium hafniense in complex with methyl-tetrahydrofolate (P21)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6SJ8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8293100 mM TRIS, 28% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
1.9235.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.4α = 90
b = 73.1β = 113.36
c = 89.76γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-04-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.553097.20.0710.9978.13.1139692
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.650.5570.8232.2

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 REPLACEMENTTHROUGHOUT6SJ81.5530132691698497.310.21940.20950.2433RANDOM21.902
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]
-3.131.15-1.752.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.596
r_dihedral_angle_4_deg15.966
r_dihedral_angle_3_deg13.928
r_dihedral_angle_1_deg6.168
r_angle_other_deg1.286
r_angle_refined_deg1.276
r_rigid_bond_restr0.547
r_chiral_restr0.058
r_bond_refined_d0.004
r_gen_planes_refined0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.596
r_dihedral_angle_4_deg15.966
r_dihedral_angle_3_deg13.928
r_dihedral_angle_1_deg6.168
r_angle_other_deg1.286
r_angle_refined_deg1.276
r_rigid_bond_restr0.547
r_chiral_restr0.058
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9228
Nucleic Acid Atoms
Solvent Atoms402
Heterogen Atoms138

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing