5UGF

Crystal structure of human purine nucleoside phosphorylase (F159Y) mutant 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 DROP7.5295100 mM HEPES, pH 7.5, 0.2 M lithium sulfate, 25% w/v PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.0840.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.96α = 90
b = 124.27β = 90
c = 136.73γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2016-10-18MSINGLE 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)CC (Half)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
12.269.261000.170.995.86.69130324
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.241000.711.86

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 3PHB2.269.2686719449299.960.215030.213820.23809RANDOM34.993
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]
2.72-1.13-1.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.537
r_dihedral_angle_3_deg13.746
r_dihedral_angle_4_deg12.032
r_long_range_B_refined6.501
r_long_range_B_other6.501
r_dihedral_angle_1_deg6.178
r_mcangle_it3.195
r_mcangle_other3.195
r_scangle_other2.526
r_mcbond_it1.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.537
r_dihedral_angle_3_deg13.746
r_dihedral_angle_4_deg12.032
r_long_range_B_refined6.501
r_long_range_B_other6.501
r_dihedral_angle_1_deg6.178
r_mcangle_it3.195
r_mcangle_other3.195
r_scangle_other2.526
r_mcbond_it1.78
r_mcbond_other1.78
r_scbond_it1.429
r_scbond_other1.429
r_angle_refined_deg1.368
r_angle_other_deg0.931
r_chiral_restr0.075
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13348
Nucleic Acid Atoms
Solvent Atoms713
Heterogen Atoms265

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing