4D98

Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis in space group H32 at pH 7.5


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.52910.1 M HEPES, 1%(v/v) MPD, 2 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, temperature 291K
Crystal Properties
Matthew coefficientSolvent content
2.0540.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 158.26α = 90
b = 158.26β = 90
c = 93.867γ = 120
Symmetry
Space GroupH 3 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
11.73095.50.09311.5847177
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)
11.71.7692.60.38274538

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 REPLACEMENTTHROUGHOUT1.729.8146951237595.070.170.16820.2059RANDOM24.0276
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.358
r_dihedral_angle_4_deg17.658
r_dihedral_angle_3_deg13.781
r_dihedral_angle_1_deg5.816
r_scangle_it5.046
r_scbond_it2.956
r_mcangle_it1.727
r_angle_refined_deg1.557
r_mcbond_it0.949
r_chiral_restr0.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.358
r_dihedral_angle_4_deg17.658
r_dihedral_angle_3_deg13.781
r_dihedral_angle_1_deg5.816
r_scangle_it5.046
r_scbond_it2.956
r_mcangle_it1.727
r_angle_refined_deg1.557
r_mcbond_it0.949
r_chiral_restr0.107
r_bond_refined_d0.016
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3522
Nucleic Acid Atoms
Solvent Atoms334
Heterogen Atoms18

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling