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Crystal structure of glycine sarcosine N-methyltransferase from Methanohalophilus portucalensis in complex with S-adenosylmethionine and sarcosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HIL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 277.15 Protein solution: GSMT (6.6 mg/ml) in 100 mM TES pH 7.3, 2 M KCl, 1 mM EDTA, 1 mM 2-Mercaptoethanol, 0.1 mM SAH and 0.2 M sarcosine.
Crystallization reagent: 0.2 M Potassium sodium tartrate tetrahydrate and 20% (w/v) Polyethylene Glycol 3350. 2 mM SAM and 685 mM sarcosine were soaked into crystals before data collection
Crystal Properties Matthews coefficient Solvent content 3.12 65.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.733 α = 90 b = 120.71 β = 90 c = 130.922 γ = 90
Symmetry Space Group I 2 2 2
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 ADSC QUANTUM 315r 2016-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 0.97622 NSRRC BL13C1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.205 29.195 97.98 18.075 3.5 20701
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5HIL 2.205 29.195 1.34 20698 1039 97.98 0.175 0.1734 0.2036 0.2155
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 12.091 f_angle_d 0.815 f_chiral_restr 0.05 f_bond_d 0.007 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1984 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 49
Software Software Software Name Purpose PHENIX refinement Blu-Ice data collection HKL-2000 data scaling HKL-2000 data processing PHENIX model building HKL-2000 data reduction PHENIX phasing