4DAB

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


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
2.7855.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.394α = 90
b = 135.394β = 90
c = 58.006γ = 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
11.855097.20.05716.76.926504
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)
11.851.92910.5116.42432

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 REPLACEMENTTHROUGHOUT1.8541.2326282131496.480.20270.20070.2412RANDOM29.7274
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]
0.020.010.02-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.689
r_dihedral_angle_4_deg20.148
r_dihedral_angle_3_deg14.385
r_dihedral_angle_1_deg5.875
r_scangle_it4.382
r_scbond_it2.627
r_mcangle_it1.539
r_angle_refined_deg1.528
r_mcbond_it0.856
r_chiral_restr0.115
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.689
r_dihedral_angle_4_deg20.148
r_dihedral_angle_3_deg14.385
r_dihedral_angle_1_deg5.875
r_scangle_it4.382
r_scbond_it2.627
r_mcangle_it1.539
r_angle_refined_deg1.528
r_mcbond_it0.856
r_chiral_restr0.115
r_bond_refined_d0.016
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1761
Nucleic Acid Atoms
Solvent Atoms130
Heterogen Atoms33

Software

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