7ZSN

human purine nucleoside phosphorylase in complex with JS-379


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7ZSL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291.1515.00 % w/v Polyethylene glycol 8,000; 500 mM Lithium sulfate; 100 mM Sodium acetate; pH 4.6; 1 mM TEW
Crystal Properties
Matthews coefficientSolvent content
74.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 141.72α = 90
b = 141.72β = 90
c = 162.44γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.3649.0199.90.9997.8910.1850135
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)
12.362.50.351

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 REPLACEMENTTHROUGHOUT7ZSL2.3649.0124922109099.90.2220.22040.2587RANDOM66.426
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]
-0.17-0.09-0.170.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.045
r_dihedral_angle_4_deg20.02
r_dihedral_angle_3_deg15.563
r_dihedral_angle_1_deg7.234
r_angle_refined_deg1.597
r_angle_other_deg1.229
r_chiral_restr0.058
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.045
r_dihedral_angle_4_deg20.02
r_dihedral_angle_3_deg15.563
r_dihedral_angle_1_deg7.234
r_angle_refined_deg1.597
r_angle_other_deg1.229
r_chiral_restr0.058
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.004
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2138
Nucleic Acid Atoms
Solvent Atoms38
Heterogen Atoms122

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing