5I3C

Crystal structure of E.coli purine nucleoside phosphorylase with acycloguanosine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4RJ2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIQUID DIFFUSION294ammonium sulphate
Crystal Properties
Matthews coefficientSolvent content
3.2161.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.03α = 90
b = 120.03β = 90
c = 238.141γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU0.8SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.323098.660.0977.0045.5544040
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)
12.322.4593.720.282.663.68

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 REPLACEMENTTHROUGHOUT4RJ22.3229.9541823215298.50.178060.176130.21664RANDOM32.911
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.928
r_dihedral_angle_4_deg21.145
r_dihedral_angle_3_deg15.514
r_dihedral_angle_1_deg7.005
r_long_range_B_refined5.65
r_long_range_B_other5.639
r_scangle_other3.724
r_mcangle_it3.419
r_mcangle_other3.418
r_scbond_it2.212
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.928
r_dihedral_angle_4_deg21.145
r_dihedral_angle_3_deg15.514
r_dihedral_angle_1_deg7.005
r_long_range_B_refined5.65
r_long_range_B_other5.639
r_scangle_other3.724
r_mcangle_it3.419
r_mcangle_other3.418
r_scbond_it2.212
r_scbond_other2.208
r_mcbond_it2.022
r_mcbond_other2.021
r_angle_refined_deg1.495
r_angle_other_deg0.97
r_chiral_restr0.087
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms5391
Nucleic Acid Atoms
Solvent Atoms134
Heterogen Atoms73

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing