2Q7O

Structure of human purine nucleoside phosphorylase in complex with L-Immucillin-H


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP52981.8 M Ammonium dihydrogen phosphate, 100 mM sodium citrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
5.1175.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 143.457α = 90
b = 143.457β = 90
c = 166.248γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-09-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.07200NSLSX29A

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
12.93599.90.1020.0737.58.8147551474182
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)
12.9399.30.8450.731.46.51442

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT1rr62.934.54147361472874599.940.2180.2180.2160.262RANDOM71.358
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]
0.130.060.13-0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.405
r_dihedral_angle_3_deg24.583
r_dihedral_angle_4_deg24.151
r_dihedral_angle_1_deg12.518
r_scangle_it4.281
r_angle_refined_deg2.953
r_scbond_it2.748
r_mcangle_it2.027
r_mcbond_it1.258
r_nbtor_refined0.354
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.405
r_dihedral_angle_3_deg24.583
r_dihedral_angle_4_deg24.151
r_dihedral_angle_1_deg12.518
r_scangle_it4.281
r_angle_refined_deg2.953
r_scbond_it2.748
r_mcangle_it2.027
r_mcbond_it1.258
r_nbtor_refined0.354
r_nbd_refined0.321
r_symmetry_vdw_refined0.307
r_xyhbond_nbd_refined0.196
r_chiral_restr0.181
r_symmetry_hbond_refined0.101
r_bond_refined_d0.033
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2223
Nucleic Acid Atoms
Solvent Atoms21
Heterogen Atoms24

Software

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