5H02

Crystal structure of Methanohalophilus portucalensis glycine sarcosine N-methyltransferase tetramutant (H21G, E23T, E24N, L28S)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5HIL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.3277.15Protein 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 coefficientSolvent content
3.1661.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.874α = 90
b = 120.803β = 90
c = 131.301γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2014-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A11.00000NSRRCBL15A1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.7762010031.5184.940112
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.781.82

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5HIL1.77619.8881.3540110199599.660.17750.17650.1958
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d16.015
f_angle_d0.796
f_chiral_restr0.053
f_bond_d0.006
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2007
Nucleic Acid Atoms
Solvent Atoms173
Heterogen Atoms42

Software

Software
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
HKL-2000data scaling
HKL-2000data processing
PHENIXmodel building
HKL-2000data reduction
PHENIXphasing