4GKA

Crystal structure of purine nucleoside phosphorylase (W16Y, W94Y, W178Y, H257W) mutant from human complexed with phosphate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.2M zinc acetate, 10% (v/v) 2-propanol, 0.1M sodium cacodylate , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0239.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.882α = 90
b = 233.67β = 97.33
c = 70.077γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2012-04-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.075NSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.2501000.1030.10319.44.2863498634933
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.281000.8760.8762.14.28627

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.245.298629681976432099.560.190230.190230.187980.23204RANDOM47.737
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]
4.64-0.69-0.84-3.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.948
r_dihedral_angle_4_deg14.783
r_dihedral_angle_3_deg13.211
r_dihedral_angle_1_deg6.067
r_angle_refined_deg1.399
r_angle_other_deg0.801
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_other0.008
r_gen_planes_refined0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.948
r_dihedral_angle_4_deg14.783
r_dihedral_angle_3_deg13.211
r_dihedral_angle_1_deg6.067
r_angle_refined_deg1.399
r_angle_other_deg0.801
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_other0.008
r_gen_planes_refined0.006
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12575
Nucleic Acid Atoms
Solvent Atoms404
Heterogen Atoms42

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-3000data reduction
SCALEPACKdata scaling