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Crystal structure of Methanohalophilus portucalensis glycine sarcosine N-methyltransferase tetramutant (H21G, E23T, E24N, L28S)
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 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 50 mM glycine.
Crystallization reagent: 0.2 M Ammonium phosphate monobasic. 0.23 M ammonia phosphate monobasic, 0.1 mM SAH and 3.35 M betaine were used as cryoprotectant before data collection
Crystal Properties Matthews coefficient Solvent content 3.16 61.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.874 α = 90 b = 120.803 β = 90 c = 131.301 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 RAYONIX MX300HE 2014-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.00000 NSRRC BL15A1
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 1.776 20 100 31.518 4.9 40112
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 1.78 1.82
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 1.776 19.888 1.35 40110 1995 99.66 0.1775 0.1765 0.1958 0.2087
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 16.015 f_angle_d 0.796 f_chiral_restr 0.053 f_bond_d 0.006 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2007 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 42
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