5TC7

Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with 5'-methylthiotubercidin at 1.75 angstrom


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 (0.2 M lithium sulfate, 0.1 M TRIS pH 8.5 and 20% (w/v) PEG 4000)
Crystal Properties
Matthews coefficientSolvent content
2.9558.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.359α = 90
b = 123.359β = 90
c = 44.499γ = 120
Symmetry
Space GroupP 3 2 1

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
11.745099.40.0830.08718.6411.0739581-329.869
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.741.8598.50.7290.7653.0911.13

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 REPLACEMENTTHROUGHOUT1K271.752537326196599.590.17020.16950.1843RANDOM27.994
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]
0.490.250.49-1.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.519
r_dihedral_angle_4_deg14.658
r_dihedral_angle_3_deg13.74
r_dihedral_angle_1_deg6.125
r_mcangle_it2.917
r_mcbond_it1.768
r_mcbond_other1.766
r_angle_refined_deg1.461
r_angle_other_deg0.957
r_chiral_restr0.074
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.519
r_dihedral_angle_4_deg14.658
r_dihedral_angle_3_deg13.74
r_dihedral_angle_1_deg6.125
r_mcangle_it2.917
r_mcbond_it1.768
r_mcbond_other1.766
r_angle_refined_deg1.461
r_angle_other_deg0.957
r_chiral_restr0.074
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2096
Nucleic Acid Atoms
Solvent Atoms189
Heterogen Atoms36

Software

Software
Software NamePurpose
XDSdata reduction
XDSdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction