5TC5

Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with butylthio-DADMe-Immucillin-A and chloride


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1K27 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5295Protein (15 mg/mL); Reservoir (3 M sodium chloride and 0.1 M sodium acetate (pH 4.5))
Crystal Properties
Matthews coefficientSolvent content
2.6453.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.522α = 90
b = 121.927β = 90
c = 192.522γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2015-02-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.97931APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.965099.70.0740.0816.867.4875649-339.471
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)
11.962.08990.7822.777.48

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT1K271.962571803377999.760.1910.18960.2166RANDOM51.803
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]
-2.521.540.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.766
r_dihedral_angle_4_deg17.184
r_dihedral_angle_3_deg13.663
r_dihedral_angle_1_deg6.417
r_mcangle_it3.466
r_mcbond_it2.492
r_mcbond_other2.491
r_angle_refined_deg1.858
r_angle_other_deg1.605
r_chiral_restr0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.766
r_dihedral_angle_4_deg17.184
r_dihedral_angle_3_deg13.663
r_dihedral_angle_1_deg6.417
r_mcangle_it3.466
r_mcbond_it2.492
r_mcbond_other2.491
r_angle_refined_deg1.858
r_angle_other_deg1.605
r_chiral_restr0.12
r_bond_refined_d0.018
r_gen_planes_refined0.011
r_bond_other_d0.009
r_gen_planes_other0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6261
Nucleic Acid Atoms
Solvent Atoms228
Heterogen Atoms73

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction