2P02

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QM4PDB entry 1QM4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82980.2M 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 coefficientSolvent content
2.1542.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.301α = 90
b = 94.106β = 90
c = 117.383γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-06-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.97600SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.2173.52990.050123.097.16113895113895
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.211.397.50.184910.936.48

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1QM41.2173.52108185108185570999.010.10080.10080.099810.11946RANDOM7.3
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.312
r_dihedral_angle_4_deg21.319
r_dihedral_angle_3_deg11.051
r_sphericity_free7.745
r_dihedral_angle_1_deg6.622
r_scangle_it3.736
r_sphericity_bonded3.117
r_scbond_it2.894
r_mcangle_it1.944
r_angle_refined_deg1.615
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.312
r_dihedral_angle_4_deg21.319
r_dihedral_angle_3_deg11.051
r_sphericity_free7.745
r_dihedral_angle_1_deg6.622
r_scangle_it3.736
r_sphericity_bonded3.117
r_scbond_it2.894
r_mcangle_it1.944
r_angle_refined_deg1.615
r_mcbond_it1.576
r_rigid_bond_restr1.258
r_angle_other_deg0.993
r_mcbond_other0.546
r_symmetry_vdw_other0.261
r_nbd_refined0.228
r_nbd_other0.203
r_nbtor_refined0.18
r_xyhbond_nbd_refined0.179
r_symmetry_vdw_refined0.15
r_symmetry_hbond_refined0.15
r_chiral_restr0.103
r_nbtor_other0.089
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_bond_other_d0.003
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms3030
Nucleic Acid Atoms
Solvent Atoms524
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing