4DA6

Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis in complex with ganciclovir


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
Matthew coefficientSolvent content
2.7855.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.551α = 90
b = 135.551β = 90
c = 57.772γ = 120
Symmetry
Space GroupP 63 2 2

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 Merge 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
11.75098.40.06616.88.834286
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7698.30.4554.83352

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 REPLACEMENTTHROUGHOUT1.741.1734157171798.050.17880.17760.2039RANDOM28.781
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]
0.010.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.741
r_dihedral_angle_3_deg13.356
r_dihedral_angle_4_deg8.438
r_dihedral_angle_1_deg5.963
r_scangle_it4.048
r_scbond_it2.413
r_mcangle_it1.513
r_angle_refined_deg1.473
r_mcbond_it0.837
r_chiral_restr0.109
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.741
r_dihedral_angle_3_deg13.356
r_dihedral_angle_4_deg8.438
r_dihedral_angle_1_deg5.963
r_scangle_it4.048
r_scbond_it2.413
r_mcangle_it1.513
r_angle_refined_deg1.473
r_mcbond_it0.837
r_chiral_restr0.109
r_bond_refined_d0.014
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1761
Nucleic Acid Atoms
Solvent Atoms154
Heterogen Atoms33

Software

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