4DAN

Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis in complex with 2-fluoroadenosine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION4.62910.1 M sodium acetate, 3.2 M sodium chloride, 5%(v/v) glycerol, pH 4.6, vapor diffusion, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.6653.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.804α = 90
b = 135.804β = 90
c = 55.154γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE W01B-MX2LNLSW01B-MX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.564093.70.10412.34.41777017770
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)
12.562.793.70.3030.3032.14.42561

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.56201773394392.80.15960.15660.211RANDOM23.5882
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]
-12.58-12.5825.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.958
r_dihedral_angle_3_deg14.896
r_dihedral_angle_4_deg14.161
r_dihedral_angle_1_deg6.836
r_scangle_it2.62
r_scbond_it1.584
r_angle_refined_deg1.407
r_mcangle_it1.117
r_angle_other_deg0.888
r_mcbond_it0.588
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.958
r_dihedral_angle_3_deg14.896
r_dihedral_angle_4_deg14.161
r_dihedral_angle_1_deg6.836
r_scangle_it2.62
r_scbond_it1.584
r_angle_refined_deg1.407
r_mcangle_it1.117
r_angle_other_deg0.888
r_mcbond_it0.588
r_mcbond_other0.095
r_chiral_restr0.071
r_bond_refined_d0.013
r_bond_other_d0.006
r_gen_planes_refined0.005
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3509
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms40

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction