6SJP

Methyltransferase of the MtgA N227A mutant from Desulfitobacterium hafniense


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293100 mM HEPES, 27% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.0740.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.04α = 90
b = 83.86β = 90
c = 86.63γ = 90
Symmetry
Space GroupP 21 21 21

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
11.93098.10.1260.9927.5443506
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)
11.920.570.8893

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 REPLACEMENTTHROUGHOUT6SJ81.93041319217598.090.19140.18970.2237RANDOM23.403
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]
4.45-2.57-1.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.548
r_dihedral_angle_4_deg16.221
r_dihedral_angle_3_deg13.509
r_dihedral_angle_1_deg6.204
r_angle_refined_deg1.264
r_angle_other_deg1.212
r_rigid_bond_restr0.678
r_chiral_restr0.056
r_bond_refined_d0.004
r_gen_planes_refined0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.548
r_dihedral_angle_4_deg16.221
r_dihedral_angle_3_deg13.509
r_dihedral_angle_1_deg6.204
r_angle_refined_deg1.264
r_angle_other_deg1.212
r_rigid_bond_restr0.678
r_chiral_restr0.056
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4702
Nucleic Acid Atoms
Solvent Atoms141
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
REFMACphasing