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Methyltransferase of the MtgA N227A mutant from Desulfitobacterium hafniense in complex with methyl-tetrahydrofolate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SJ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 100 mM HEPES, 27% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.1 41.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.16 α = 90 b = 84.26 β = 90 c = 86.71 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2019-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.8 30 98.1 0.093 0.996 8.6 3.7 51389
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) Redundancy Number Unique Reflections (All) 1 1.8 1.9 0.595 0.726 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6SJ8 1.8 30 48810 2569 98.1 0.1817 0.1798 0.2196 0.2227 RANDOM 22.296
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] 0.9 -2.07 1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.353 r_dihedral_angle_4_deg 15.837 r_dihedral_angle_3_deg 12.554 r_dihedral_angle_1_deg 5.828 r_angle_refined_deg 1.198 r_angle_other_deg 1.184 r_rigid_bond_restr 0.478 r_chiral_restr 0.048 r_bond_refined_d 0.003 r_gen_planes_refined 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.353 r_dihedral_angle_4_deg 15.837 r_dihedral_angle_3_deg 12.554 r_dihedral_angle_1_deg 5.828 r_angle_refined_deg 1.198 r_angle_other_deg 1.184 r_rigid_bond_restr 0.478 r_chiral_restr 0.048 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4680 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling REFMAC phasing