2ON6

Crystal structure of human purine nucleoside phosphorylase mutant H257F with Imm-H


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62980.1 M Sodium Acetate, 4.0 M Ammonium Acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 142.856α = 90
b = 142.856β = 90
c = 167.995γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-05-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.100NSLSX29A

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
12.5033094.50.0710.07110.57230142163472
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)
12.5032.5983.30.4250.3781.83.81870

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 REPLACEMENTTHROUGHOUT2.50329.532288221629111494.520.2030.2030.2010.245RANDOM64.409
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.444
r_dihedral_angle_4_deg22.229
r_dihedral_angle_3_deg20.077
r_dihedral_angle_1_deg7.724
r_scangle_it4.61
r_scbond_it2.935
r_angle_refined_deg2.227
r_mcangle_it2.163
r_mcbond_it1.298
r_nbtor_refined0.331
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.444
r_dihedral_angle_4_deg22.229
r_dihedral_angle_3_deg20.077
r_dihedral_angle_1_deg7.724
r_scangle_it4.61
r_scbond_it2.935
r_angle_refined_deg2.227
r_mcangle_it2.163
r_mcbond_it1.298
r_nbtor_refined0.331
r_nbd_refined0.258
r_symmetry_vdw_refined0.186
r_xyhbond_nbd_refined0.169
r_symmetry_hbond_refined0.163
r_chiral_restr0.127
r_bond_refined_d0.022
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2214
Nucleic Acid Atoms
Solvent Atoms64
Heterogen Atoms19

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling