3GGD

Crystal structure of SAM-dependent methyltransferase (YP_325210.1) from ANABAENA VARIABILIS ATCC 29413 at 2.11 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.01M cobalt chloride, 1.8M ammonium sulfate, 0.1M MES pH 6.5, ADDITIVE: 0.001 M S-ADENOSYLMETHIONINE (SAM), NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.52	α = 90
b = 112.52	β = 90
c = 112.56	γ = 90

Symmetry
Space Group	P 41 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	Adjustable focusing mirrors in K-B geometry	2008-10-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.94645,0.97967	APS	23-ID-B

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	2.11	30.083	99.7	0.221	11	17.9		42096		-3	40.16

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	2.11	2.19	99.6		1.53	2

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	MAD	THROUGHOUT	2.11	30.083	42037	2128	99.77	0.163	0.162	0.175	RANDOM	63.133

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]
0.95			0.95		-1.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.854
r_dihedral_angle_4_deg	15.286
r_dihedral_angle_3_deg	11.287
r_dihedral_angle_1_deg	5.251
r_scangle_it	3.204
r_scbond_it	2.301
r_angle_refined_deg	1.646
r_mcangle_it	1.302
r_angle_other_deg	0.947
r_mcbond_it	0.923
r_symmetry_vdw_refined	0.288
r_mcbond_other	0.217
r_nbd_refined	0.216
r_symmetry_hbond_refined	0.21
r_nbd_other	0.204
r_nbtor_refined	0.187
r_symmetry_vdw_other	0.184
r_xyhbond_nbd_refined	0.18
r_chiral_restr	0.096
r_nbtor_other	0.089
r_xyhbond_nbd_other	0.043
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1912
Nucleic Acid Atoms
Solvent Atoms	192
Heterogen Atoms	98

Software

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