5TC6

Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with propylthio-immucillin-A


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 (0.17 M sodium acetate, 85 mM Tris:HCl (pH 8.5), 25% (w/v) PEG 4000 and 15% (v/v) glycerol)
Crystal Properties
Matthews coefficientSolvent content
2.9257.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.76α = 90
b = 122.76β = 90
c = 44.484γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-09-12MSINGLE 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)Rrim I (All)Rpim 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
11.48501000.0790.0830.02410.211.56427711.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.481.511000.8760.825310.7

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 REPLACEMENTTHROUGHOUT1K271.482561028317799.930.1680.16710.1849RANDOM19.003
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]
0.080.040.08-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.087
r_dihedral_angle_4_deg14.326
r_dihedral_angle_3_deg13.004
r_dihedral_angle_1_deg5.656
r_mcangle_it1.698
r_scbond_it1.49
r_angle_refined_deg1.432
r_mcbond_it0.983
r_chiral_restr0.075
r_bond_refined_d0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.087
r_dihedral_angle_4_deg14.326
r_dihedral_angle_3_deg13.004
r_dihedral_angle_1_deg5.656
r_mcangle_it1.698
r_scbond_it1.49
r_angle_refined_deg1.432
r_mcbond_it0.983
r_chiral_restr0.075
r_bond_refined_d0.008
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2105
Nucleic Acid Atoms
Solvent Atoms222
Heterogen Atoms35

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction