4JOS

Crystal structure of a putative 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Francisella philomiragia ATCC 25017 (Target NYSGRC-029335)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5298Protein (20mM HEPES pH7.5, 150mM NaCl, 5% glycerol, and 5mM DTT); Reservoir (MCSG1 #13; G10: 0.6 M Sodium Chloride, 0.1 M MES:NaOH pH 6.5, 20% (w/v) PEG 4000 )); Cryoprotection (30% Ethylene glycol), temperature 298K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.1442.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.747α = 90
b = 74.937β = 90
c = 114.542γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HEMIRRORS2013-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.9793APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.455099.70.11921.0614.88555512.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.4899.20.8472.8814.54211

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.4529.0685484216499.680.1520.15140.1747RANDOM16.2734
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]
1.04-0.04-1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.773
r_dihedral_angle_4_deg15.19
r_dihedral_angle_3_deg12.913
r_dihedral_angle_1_deg5.812
r_angle_refined_deg1.504
r_angle_other_deg0.777
r_chiral_restr0.087
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.773
r_dihedral_angle_4_deg15.19
r_dihedral_angle_3_deg12.913
r_dihedral_angle_1_deg5.812
r_angle_refined_deg1.504
r_angle_other_deg0.777
r_chiral_restr0.087
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3525
Nucleic Acid Atoms
Solvent Atoms418
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-3000data reduction
SCALEPACKdata scaling
SHELXphasing
SHELXDphasing
SHELXEmodel building