2O8R

Crystal Structure of Polyphosphate Kinase from Porphyromonas Gingivalis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72942.6M MALIC ACID, PH 7.0, 0.5M AMMONIUM SULFATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties
Matthews coefficientSolvent content
2.9157.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.33α = 90
b = 99.33β = 90
c = 335.061γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMIRRORS2006-11-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.9793APS31-ID

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
12.75097.60.0890.0964.5511995119962.3
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)
2.72.894.10.360.481.83.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT2.7204916949169157899.430.190040.190040.18790.25457RANDOM72.398
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]
0.820.410.82-1.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.003
r_dihedral_angle_3_deg19.929
r_dihedral_angle_4_deg17.639
r_scangle_it16.841
r_scbond_it13.353
r_mcangle_it10.771
r_mcbond_it8.305
r_dihedral_angle_1_deg7.144
r_angle_refined_deg1.301
r_nbtor_refined0.322
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.003
r_dihedral_angle_3_deg19.929
r_dihedral_angle_4_deg17.639
r_scangle_it16.841
r_scbond_it13.353
r_mcangle_it10.771
r_mcbond_it8.305
r_dihedral_angle_1_deg7.144
r_angle_refined_deg1.301
r_nbtor_refined0.322
r_symmetry_hbond_refined0.189
r_nbd_refined0.187
r_symmetry_vdw_refined0.174
r_xyhbond_nbd_refined0.173
r_chiral_restr0.088
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10331
Nucleic Acid Atoms
Solvent Atoms56
Heterogen Atoms65

Software

Software
Software NamePurpose
SHELXmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing