5XZ7

Crystal Structure of Phosphofructokinase from Staphylococcus aureus in complex with adenylylimidodiphosphate, the ATP analogue


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP28315% PEG4000, 0.1M MES PH 6.0 , 0.15M(NH4)2SO4
Crystal Properties
Matthews coefficientSolvent content
2.5651.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.56α = 90
b = 80.2β = 90
c = 121.3γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.9793SSRFBL17U1

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
11.666.91000.10711.66.24752112.6
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)
11.61.691000.4174.35.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT5XOE1.666.945110240499.930.155140.153890.17881RANDOM15.544
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]
0.56-0.23-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.488
r_dihedral_angle_4_deg14.811
r_dihedral_angle_3_deg12.535
r_long_range_B_refined6.053
r_long_range_B_other6.053
r_dihedral_angle_1_deg5.028
r_scangle_other4.496
r_scbond_it3.07
r_scbond_other3.07
r_mcangle_other2.341
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.488
r_dihedral_angle_4_deg14.811
r_dihedral_angle_3_deg12.535
r_long_range_B_refined6.053
r_long_range_B_other6.053
r_dihedral_angle_1_deg5.028
r_scangle_other4.496
r_scbond_it3.07
r_scbond_other3.07
r_mcangle_other2.341
r_mcangle_it2.336
r_angle_refined_deg2.217
r_mcbond_it1.653
r_mcbond_other1.64
r_angle_other_deg1.149
r_chiral_restr0.141
r_bond_refined_d0.026
r_gen_planes_refined0.011
r_bond_other_d0.004
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2446
Nucleic Acid Atoms
Solvent Atoms284
Heterogen Atoms59

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing