5BP7

Crystal structure of SAM-dependent methyltransferase from Geobacter sulfurreducens in complex with S-Adenosyl-L-homocysteine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	0.2 ul of 15 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG Suite 1 condition #9 (0.1M HEPES, 25%w/v PEG 3350, 0.2M Magnesium Chloride, 6-Hydrate pH=7.5) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 5 mM S-adenosylmethionine chloride and 1/50 v/v of 1 mg/ml TEV solution at 289 K for 3 hours

Crystal Properties
Matthews coefficient	Solvent content
2.28	41.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.346	α = 90
b = 110.189	β = 90
c = 76.681	γ = 90

Symmetry
Space Group	P 21 21 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	MARMOSAIC 300 mm CCD	Beryllium Lenses	2015-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	2.1	50	99.9	0.123	0.123	0.13	0.054	5.1	6.1	45134	45102		-3	33.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.14	100		0.995	0.444	0.756	1.6	6	2223

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.1	50	42695	2191	99.93	0.1873	0.1855	0.2229	RANDOM	40.658

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]
-1.99			-0.58		2.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.691
r_dihedral_angle_4_deg	19.425
r_dihedral_angle_3_deg	13.828
r_dihedral_angle_1_deg	5.938
r_angle_refined_deg	1.458
r_mcangle_it	1.285
r_angle_other_deg	1.196
r_mcbond_it	0.798
r_mcbond_other	0.796
r_chiral_restr	0.075

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.691
r_dihedral_angle_4_deg	19.425
r_dihedral_angle_3_deg	13.828
r_dihedral_angle_1_deg	5.938
r_angle_refined_deg	1.458
r_mcangle_it	1.285
r_angle_other_deg	1.196
r_mcbond_it	0.798
r_mcbond_other	0.796
r_chiral_restr	0.075
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.006
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5665
Nucleic Acid Atoms
Solvent Atoms	419
Heterogen Atoms	80

Software

Software
Software Name	Purpose
PDB_EXTRACT	data extraction
REFMAC	refinement
HKL-3000	phasing
MLPHARE	phasing
SHELX	phasing
HKL-3000	data scaling
HKL-3000	data reduction
BLU-MAX	data collection

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.