5ETJ

Crystal structure of purine nucleoside phosphorylase (E258D, L261A) mutant from human complexed with DADMe-ImmG and phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3PHBPDB entry 3PHB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5295Protein (10 mg/mL); Reservoir (0.2 M lithium sulfate, 0.1 M TRIS-HCl, pH 8.5 and 20% (w/v) PEG 4000)
Crystal Properties
Matthews coefficientSolvent content
2.9157.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 268.808α = 90
b = 58.845β = 112.92
c = 173.155γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2015-11-04MSINGLE 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 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
12.35099.20.09516.37.4711227210599646
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)
12.32.4396.40.7772.827.51

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 REPLACEMENTTHROUGHOUTPDB entry 3PHB2.325105996557999.80.17970.17810.2109RANDOM43.583
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]
-1.45-0.572.4-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.902
r_dihedral_angle_4_deg17.245
r_dihedral_angle_3_deg15.078
r_dihedral_angle_1_deg6.477
r_mcangle_it3.887
r_mcbond_it2.518
r_mcbond_other2.518
r_angle_refined_deg1.527
r_angle_other_deg0.96
r_chiral_restr0.085
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.902
r_dihedral_angle_4_deg17.245
r_dihedral_angle_3_deg15.078
r_dihedral_angle_1_deg6.477
r_mcangle_it3.887
r_mcbond_it2.518
r_mcbond_other2.518
r_angle_refined_deg1.527
r_angle_other_deg0.96
r_chiral_restr0.085
r_bond_refined_d0.011
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 Atoms13365
Nucleic Acid Atoms
Solvent Atoms352
Heterogen Atoms180

Software

Software
Software NamePurpose
XDSdata reduction
XDSdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction