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Crystal structure of glycine sarcosine N-methyltransferase from Methanohalophilus portucalensis in complex with S-adenosylhomocysteine and sarcosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XVA PDB ENTRY 1XVA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 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 betaine.
Crystallization reagent: 0.1 M Tris-HCl pH 8.5 and 1.5 M sodium chloride.
SAH and sarcosine were soaked into crystals before data collection.
Crystal Properties Matthews coefficient Solvent content 3.15 60.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.897 α = 90 b = 121.124 β = 90 c = 131.589 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 210 2012-12-20 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) R Sym I (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 2.47 30 99 0.086 13.6 3.4 15131
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 2.47 2.6 100 2.6 3.4
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB ENTRY 1XVA 2.471 24.914 1.36 15129 762 99.01 0.1691 0.1664 0.1722 0.2184 0.2201 Random selection
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 14.017 f_angle_d 1.038 f_chiral_restr 0.039 f_bond_d 0.008 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1935 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 52
Software Software Software Name Purpose PHENIX refinement Blu-Ice data collection HKL-2000 data scaling HKL-2000 data processing PHENIX model building