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Ergothioneine-biosynthetic methyltransferase EgtD in complex with N,N-dimethylhistidine and SAH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PIM PDB entry 4PIM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.2 M magnesium chloride, 0.1 M Tris-HCl, pH 8.5, 30% w/v PEG4000
Crystal Properties Matthews coefficient Solvent content 2.05 39.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.709 α = 90 b = 67.511 β = 110.98 c = 79.679 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 CCD MARMOSAIC 225 mm CCD 2012-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.506 49.995 98.8 0.088 0.106 0.059 8.9 3.2 87536 87536 10.76
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.51 1.59 95.9 0.551 0.551 0.369 1.4 3.1 12354
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 4PIM 1.506 49.995 1.36 87509 4356 98.65 0.1497 0.1481 0.1495 0.1798 0.1797 15.5812
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.677 f_angle_d 1.278 f_chiral_restr 0.047 f_bond_d 0.008 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4823 Nucleic Acid Atoms Solvent Atoms 985 Heterogen Atoms 148
Software Software Software Name Purpose PHENIX refinement XDS data scaling SCALA data scaling MOLREP phasing PDB_EXTRACT data extraction