4F1W

Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Salmonella enterica with Adenine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3O4Vpdb entry 3O4V

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82931.0M (NH4)2HPO4, 0.1M Imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9235.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.05α = 90
b = 68.12β = 90
c = 89.66γ = 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 mirror2011-08-25MSINGLE 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
11.3654.241000.1120.11212.911.5874598745912.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.361.4399.92.611.212605

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 3O4V1.3641.958738183002437999.940.114550.114550.112860.14597RANDOM15.932
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]
-0.63-0.040.68
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free38.373
r_dihedral_angle_2_deg36.4
r_dihedral_angle_4_deg19.272
r_dihedral_angle_3_deg11.74
r_sphericity_bonded10.401
r_dihedral_angle_1_deg5.584
r_rigid_bond_restr2.186
r_angle_refined_deg1.435
r_angle_other_deg0.812
r_chiral_restr0.092
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free38.373
r_dihedral_angle_2_deg36.4
r_dihedral_angle_4_deg19.272
r_dihedral_angle_3_deg11.74
r_sphericity_bonded10.401
r_dihedral_angle_1_deg5.584
r_rigid_bond_restr2.186
r_angle_refined_deg1.435
r_angle_other_deg0.812
r_chiral_restr0.092
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3445
Nucleic Acid Atoms
Solvent Atoms386
Heterogen Atoms114

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling