4F2W

Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Salmonella enterica with methyl-thio-DADMe-Immucillin-A


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729335% 2-methyl-2,4-pentanediol, 0.2M sodium chloride, 0.1M Tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5351.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.41α = 90
b = 82.54β = 90
c = 93.11γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rRosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror2011-02-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.075NSLSX29A

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1261.77990.1960.1966.76.73643536435
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)RedundancyNumber Unique Reflections (All)
122.1196.80.3470.3474.16.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT246.183638034563181798.770.179110.177170.21597RANDOM16.933
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]
-0.41-0.480.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.143
r_dihedral_angle_4_deg17.634
r_dihedral_angle_3_deg12.91
r_dihedral_angle_1_deg6.111
r_angle_refined_deg1.452
r_angle_other_deg1.034
r_chiral_restr0.082
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.143
r_dihedral_angle_4_deg17.634
r_dihedral_angle_3_deg12.91
r_dihedral_angle_1_deg6.111
r_angle_refined_deg1.452
r_angle_other_deg1.034
r_chiral_restr0.082
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.004
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3467
Nucleic Acid Atoms
Solvent Atoms271
Heterogen Atoms66

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling