5ETS

S. aureus 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.95 angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5ETQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9.1281Protein 6.9 mg/mL 1 mM AMPCPP, 1 mM inhibitor, 0.182 MgCl2, 0.1 M tris chloride, 17.2%w/v PEG8000, 50 mM sodium thiocyanate
Crystal Properties
Matthews coefficientSolvent content
2.2846.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.79α = 90
b = 68.58β = 105.94
c = 52.99γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-04-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX21.0329Australian SynchrotronMX2

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
11.9540.999.80.14910724055
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)
11.95299.80.7582.97.1

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 REPLACEMENTTHROUGHOUT5ETQ1.9540.922747122899.510.190460.188980.21815RANDOM10.637
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]
-0.27-0.61.47-0.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.306
r_dihedral_angle_4_deg14.422
r_dihedral_angle_3_deg12.238
r_dihedral_angle_1_deg6.599
r_long_range_B_refined4.211
r_long_range_B_other4.211
r_angle_other_deg3.569
r_scangle_other2.623
r_angle_refined_deg1.747
r_scbond_it1.718
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.306
r_dihedral_angle_4_deg14.422
r_dihedral_angle_3_deg12.238
r_dihedral_angle_1_deg6.599
r_long_range_B_refined4.211
r_long_range_B_other4.211
r_angle_other_deg3.569
r_scangle_other2.623
r_angle_refined_deg1.747
r_scbond_it1.718
r_scbond_other1.717
r_mcangle_other1.351
r_mcangle_it1.346
r_mcbond_it0.864
r_mcbond_other0.852
r_chiral_restr0.094
r_bond_refined_d0.013
r_gen_planes_other0.01
r_gen_planes_refined0.007
r_bond_other_d
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 Atoms2506
Nucleic Acid Atoms
Solvent Atoms154
Heterogen Atoms109

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building