☰ Navigation Tabs
Methyltransferase MtgA from Desulfitobacterium hafniense in complex with methyl-tetrahydrofolate (P21)
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 8 293 100 mM TRIS, 28% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.92 35.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.4 α = 90 b = 73.1 β = 113.36 c = 89.76 γ = 90
Symmetry Space Group P 1 21 1
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 1.55 30 97.2 0.071 0.997 8.1 3.1 139692
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 1.55 1.65 0.557 0.823 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6SJ8 1.55 30 132691 6984 97.31 0.2194 0.2095 0.219 0.2433 0.2601 RANDOM 21.902
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] -3.13 1.15 -1.75 2.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.596 r_dihedral_angle_4_deg 15.966 r_dihedral_angle_3_deg 13.928 r_dihedral_angle_1_deg 6.168 r_angle_other_deg 1.286 r_angle_refined_deg 1.276 r_rigid_bond_restr 0.547 r_chiral_restr 0.058 r_bond_refined_d 0.004 r_gen_planes_refined 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.596 r_dihedral_angle_4_deg 15.966 r_dihedral_angle_3_deg 13.928 r_dihedral_angle_1_deg 6.168 r_angle_other_deg 1.286 r_angle_refined_deg 1.276 r_rigid_bond_restr 0.547 r_chiral_restr 0.058 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9228 Nucleic Acid Atoms Solvent Atoms 402 Heterogen Atoms 138
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing