3GB9

Human purine nucleoside phosphorylase double mutant E201Q,N243D complexed with 2-fluoroadenine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RFGPDB entry 1RFG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62981.54 M Ammonium sulfate, 0.05M Sodium potassium phosphate pH 6.8, 3% Trimethylamine N-oxide, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.3963.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.791α = 90
b = 130.648β = 90
c = 149.177γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.9793APS24-ID-C

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
12.35081.20.10516.9235.851620-352.4
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)
12.32.3826.80.3365.41680

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 1RFG2.35051499260581.60.1860.1840.227RANDOM32.774
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]
5.22-2.57-2.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.966
r_dihedral_angle_4_deg18.949
r_dihedral_angle_3_deg17.336
r_dihedral_angle_1_deg6.189
r_scangle_it3.637
r_mcangle_it3.566
r_scbond_it2.49
r_mcbond_it2.168
r_angle_refined_deg1.362
r_angle_other_deg0.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.966
r_dihedral_angle_4_deg18.949
r_dihedral_angle_3_deg17.336
r_dihedral_angle_1_deg6.189
r_scangle_it3.637
r_mcangle_it3.566
r_scbond_it2.49
r_mcbond_it2.168
r_angle_refined_deg1.362
r_angle_other_deg0.86
r_mcbond_other0.525
r_chiral_restr0.079
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6452
Nucleic Acid Atoms
Solvent Atoms211
Heterogen Atoms204

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction