3GGS

Human purine nucleoside phosphorylase double mutant E201Q,N243D complexed with 2-fluoro-2'-deoxyadenosine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GB9PDB entry 3GB9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62981.54M 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
3.3763.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.24α = 90
b = 130.646β = 90
c = 149.433γ = 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
12.55099.40.0917.8876.647561-357.2
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)
12.52.5998.10.396.44622

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 3GB92.525047486239598.590.2140.2120.251RANDOM52.026
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]
8.33-3.53-4.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.721
r_dihedral_angle_3_deg19.394
r_dihedral_angle_4_deg17.466
r_dihedral_angle_1_deg6.352
r_mcangle_it2.381
r_scangle_it2.091
r_scbond_it1.444
r_mcbond_it1.402
r_angle_refined_deg1.26
r_angle_other_deg0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.721
r_dihedral_angle_3_deg19.394
r_dihedral_angle_4_deg17.466
r_dihedral_angle_1_deg6.352
r_mcangle_it2.381
r_scangle_it2.091
r_scbond_it1.444
r_mcbond_it1.402
r_angle_refined_deg1.26
r_angle_other_deg0.88
r_mcbond_other0.373
r_chiral_restr0.07
r_bond_refined_d0.009
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 Atoms6614
Nucleic Acid Atoms
Solvent Atoms64
Heterogen Atoms226

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing