6SJO

Methyltransferase of the MtgA D102A mutant from Desulfitobacterium hafniense in complex with methyl-tetrahydrofolate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SJ8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293100 mM HEPES, 27% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.1442.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.03α = 90
b = 84.29β = 90
c = 87.56γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-12-01MSINGLE 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
11.953099.20.0920.99811.55.141877
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)
11.952.0599.20.5790.9172.6

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 REPLACEMENTTHROUGHOUT1SJ81.953039770209399.130.18690.18510.2174RANDOM31.928
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]
4.84-3.19-1.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.813
r_dihedral_angle_4_deg20.786
r_dihedral_angle_3_deg13.264
r_dihedral_angle_1_deg5.905
r_angle_refined_deg1.297
r_angle_other_deg1.226
r_rigid_bond_restr1.014
r_chiral_restr0.057
r_gen_planes_refined0.005
r_bond_refined_d0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.813
r_dihedral_angle_4_deg20.786
r_dihedral_angle_3_deg13.264
r_dihedral_angle_1_deg5.905
r_angle_refined_deg1.297
r_angle_other_deg1.226
r_rigid_bond_restr1.014
r_chiral_restr0.057
r_gen_planes_refined0.005
r_bond_refined_d0.004
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4679
Nucleic Acid Atoms
Solvent Atoms76
Heterogen Atoms63

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
REFMACphasing