3OFK

Crystal structure of N-methyltransferase NodS from Bradyrhizobium japonicum WM9 in complex with S-adenosyl-l-homocysteine (SAH)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	292	16% PEG 8000, 5 mM magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.01	α = 90
b = 143.3	β = 90
c = 75.85	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	MAR CCD 165 mm	mirrors	2008-03-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9184	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.85	50	96	0.052	24.6	5.04		72827		-3	39

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.92	97.8		0.347	2.4

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	R-FREE	1.85	29.7	70528	1165	100	0.19048	0.18965	0.23764	RANDOM	39.766

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]
0.64			-0.25		-0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.888
r_dihedral_angle_4_deg	17.163
r_dihedral_angle_3_deg	15.577
r_scangle_it	6.8
r_dihedral_angle_1_deg	6.185
r_scbond_it	4.512
r_mcangle_it	1.873
r_angle_refined_deg	1.706
r_mcbond_it	1.034
r_angle_other_deg	0.997
r_mcbond_other	0.267
r_chiral_restr	0.108
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6133
Nucleic Acid Atoms
Solvent Atoms	846
Heterogen Atoms	104

Software

Software
Software Name	Purpose
MAR345dtb	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling