2P02

Crystal structure of the alpha subunit of human S-adenosylmethionine synthetase 2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QM4	PDB entry 1QM4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	298	0.2M Lithium chloride, 0.1M Tris-HCl, 20% PEG 6000, 10.0% Ethylene glycol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.301	α = 90
b = 94.106	β = 90
c = 117.383	γ = 90

Symmetry
Space Group	I 2 2 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 225 mm CCD		2006-06-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.97600	SLS	X10SA

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	1.21	73.52	99	0.0501	23.09	7.16	113895	113895

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)
	1.21	1.3	97.5		0.1849	10.93	6.48

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1QM4	1.21	73.52	108185	108185	5709	99.01	0.1008	0.1008	0.09981	0.11946	RANDOM	7.3

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]
0.75			-0.57		-0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.312
r_dihedral_angle_4_deg	21.319
r_dihedral_angle_3_deg	11.051
r_sphericity_free	7.745
r_dihedral_angle_1_deg	6.622
r_scangle_it	3.736
r_sphericity_bonded	3.117
r_scbond_it	2.894
r_mcangle_it	1.944
r_angle_refined_deg	1.615
r_mcbond_it	1.576
r_rigid_bond_restr	1.258
r_angle_other_deg	0.993
r_mcbond_other	0.546
r_symmetry_vdw_other	0.261
r_nbd_refined	0.228
r_nbd_other	0.203
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.179
r_symmetry_vdw_refined	0.15
r_symmetry_hbond_refined	0.15
r_chiral_restr	0.103
r_nbtor_other	0.089
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3030
Nucleic Acid Atoms
Solvent Atoms	524
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing