3BGS

Structure of human purine nucleoside phosphorylase with L-DADMe-ImmH and phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RR6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP52910.1 M Sodium citrate pH 5.0, 2.3 M ammonium dihydrogenphosphate, Vapor diffusion, sitting drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
4.8274.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 142.801α = 90
b = 142.801β = 90
c = 167.348γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A0.9793NSLSX29A

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
12.09999.51000.0740.07613.612.53839738397
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)
2.0992.181000.7140.6272.57.73798

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 DIFFRACTIONTHROUGHOUT1RR62.09999.538395192299.890.2190.2180.249RANDOM56.149
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]
0.060.030.06-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.793
r_dihedral_angle_4_deg17.455
r_dihedral_angle_3_deg14.493
r_dihedral_angle_1_deg4.891
r_mcangle_it4.711
r_scangle_it4.634
r_mcbond_it3.392
r_scbond_it3.301
r_angle_refined_deg1.639
r_nbtor_refined0.327
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.793
r_dihedral_angle_4_deg17.455
r_dihedral_angle_3_deg14.493
r_dihedral_angle_1_deg4.891
r_mcangle_it4.711
r_scangle_it4.634
r_mcbond_it3.392
r_scbond_it3.301
r_angle_refined_deg1.639
r_nbtor_refined0.327
r_nbd_refined0.239
r_xyhbond_nbd_refined0.211
r_symmetry_hbond_refined0.191
r_symmetry_vdw_refined0.172
r_chiral_restr0.114
r_bond_refined_d0.015
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2299
Nucleic Acid Atoms
Solvent Atoms101
Heterogen Atoms34

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction