5HIJ | pdb_00005hij

Crystal structure of glycine sarcosine N-methyltransferase from Methanohalophilus portucalensis in complex with betaine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5HIL	PDB ENTRY 5HIL

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 and 1 mM 2-Mercaptoethanol. Crystallization reagent: 0.2 M Potassium sodium tartrate tetrahydrate, 20% w/v Polyethylene glycol 3,350. Betaine was soaked into crystals before data collection.

Crystal Properties
Matthews coefficient	Solvent content
3.15	60.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.176	α = 90
b = 120.545	β = 90
c = 131.368	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		2015-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL15A1	1.000	NSRRC	BL15A1

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	1.93	20	99.8	0.054	21.7	4.3		31210

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	1.93	2	100		3.3	4.3

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 5HIL	1.93	19.724	1.35	31208	1571	98.83	0.1678	0.1658	0.17	0.2078	0.21	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	12.785
f_angle_d	0.964
f_chiral_restr	0.045
f_bond_d	0.007
f_plane_restr	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1962
Nucleic Acid Atoms
Solvent Atoms	190
Heterogen Atoms	8

Software

Software
Software Name	Purpose
PHENIX	refinement
Blu-Ice	data collection
HKL-2000	data scaling
HKL-2000	data processing
PHENIX	model building

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.