3BOF

Cobalamin-dependent methionine synthase (1-566) from Thermotoga maritima complexed with Zn2+ and Homocysteine

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	25% 1,2-propanediol, 10% glycerol, 5% PEG 3000, 100 mM potasium citrate pH 4.8, 1.5% 1,2,3-heptanetriol, 10 mM YCl3. Soaking with 20% 1,2-propanediol, 10% glycerol, 5% PEG 3000, 100 mM TRIS pH 7, 1.5% 1,2,3-heptanetriol, and 10mM Hcy , VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.067	α = 90
b = 86.308	β = 100.03
c = 125.879	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	MARMOSAIC 300 mm CCD	K-B pair of biomorph mirrors for vertical and horizontal focusing	2007-04-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.9793	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.7	46.68	99.9	0.059	0.048	22.5	5.8	136668	136540			28.911

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.7	1.8	99.9		0.323	0.399	5.36	5.8	21423

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	1.7	46.68	136668	136540	6933	99.91	0.196	0.195	0.222	RANDOM	26.688

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]
0.01			0.04		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.936
r_dihedral_angle_4_deg	18.881
r_dihedral_angle_3_deg	14.951
r_dihedral_angle_1_deg	6.679
r_scangle_it	4.176
r_scbond_it	2.483
r_mcangle_it	1.606
r_angle_refined_deg	1.419
r_mcbond_it	0.864
r_nbtor_refined	0.311
r_symmetry_vdw_refined	0.24
r_nbd_refined	0.215
r_symmetry_hbond_refined	0.192
r_xyhbond_nbd_refined	0.128
r_chiral_restr	0.1
r_metal_ion_refined	0.083
r_symmetry_metal_ion_refined	0.043
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8763
Nucleic Acid Atoms
Solvent Atoms	411
Heterogen Atoms	21

Software

Software
Software Name	Purpose
XSCALE	data scaling
EPMR	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
XDS	data reduction
CNS	refinement