3BKW

Crystal structure of S-adenosylmethionine dependent methyltransferase (NP_104914.1) from Mesorhizobium loti at 1.60 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.7	277	NANODROP, 0.2M Mg Acetate, 20.0% PEG 3350, No Buffer pH 7.7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.33	α = 90
b = 58.48	β = 90
c = 142.03	γ = 90

Symmetry
Space Group	P 21 21 21

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 325 mm CCD	Flat mirror (vertical focusing)	2007-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97901	SSRL	BL11-1

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	1.6	29.235	99.8	0.072	10.55			64958		-3	26.708

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	1.6	1.66	99.1		0.725	1.4

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	THROUGHOUT	1.6	29.235	64882	3289	99.85	0.173	0.171	0.2	RANDOM	25.803

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]
-0.88			0.29		0.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.864
r_dihedral_angle_4_deg	13.382
r_dihedral_angle_3_deg	9.371
r_scangle_it	5.235
r_dihedral_angle_1_deg	4.112
r_scbond_it	3.84
r_mcangle_it	2.182
r_mcbond_it	1.81
r_angle_refined_deg	1.53
r_angle_other_deg	1.368
r_mcbond_other	0.356
r_symmetry_vdw_other	0.188
r_nbd_refined	0.177
r_nbtor_refined	0.16
r_nbd_other	0.148
r_xyhbond_nbd_refined	0.094
r_symmetry_hbond_refined	0.094
r_chiral_restr	0.093
r_nbtor_other	0.072
r_symmetry_vdw_refined	0.048
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3409
Nucleic Acid Atoms
Solvent Atoms	486
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHARP	phasing
SHELXD	phasing