1WTA

Crystal Structure of 5'-Deoxy-5'-methylthioadenosine from Aeropyrum pernix (R32 form)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.5293MPD, glycerol, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.244.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.15α = 90
b = 78.15β = 90
c = 230.43γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVmirrors2004-07-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

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
11.7876.799.40.05893.826274
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)
11.781.84990.2822.63.722594

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.7858.3624941132799.350.165550.163920.1955RANDOM15.474
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]
0.030.020.03-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.3
r_scangle_it2.423
r_scbond_it1.469
r_angle_refined_deg1.23
r_angle_other_deg1.078
r_mcangle_it0.838
r_mcbond_it0.439
r_symmetry_vdw_other0.252
r_nbd_other0.245
r_symmetry_hbond_refined0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.3
r_scangle_it2.423
r_scbond_it1.469
r_angle_refined_deg1.23
r_angle_other_deg1.078
r_mcangle_it0.838
r_mcbond_it0.439
r_symmetry_vdw_other0.252
r_nbd_other0.245
r_symmetry_hbond_refined0.21
r_nbd_refined0.189
r_symmetry_vdw_refined0.166
r_xyhbond_nbd_refined0.144
r_nbtor_other0.131
r_chiral_restr0.071
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_gen_planes_other0.005
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2133
Nucleic Acid Atoms
Solvent Atoms358
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing