5ETR

S. aureus 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.32 angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.1281Protein 6.9 mg/mL 1 mM AMPCPP, 1 mM inhibitor, 0.202 M MgCl2, 0.1 M tris chloride, 19.6%w/v PEG8000, 50 mM sodium thiocyanate
Crystal Properties
Matthews coefficientSolvent content
2.2645.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.582α = 90
b = 68.11β = 106.12
c = 53.227γ = 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
11.3245.711000.07712.87.477438
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)
11.321.341000.8322.27

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 REPLACEMENTTHROUGHOUT5ETQ1.3245.7173521388899.990.125350.123940.1518RANDOM14.485
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]
0.07-0.030.18-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.119
r_sphericity_free26.358
r_rigid_bond_restr12.948
r_dihedral_angle_3_deg11.256
r_dihedral_angle_4_deg10.871
r_sphericity_bonded7.638
r_dihedral_angle_1_deg6.149
r_angle_other_deg3.547
r_long_range_B_refined2.918
r_long_range_B_other2.747
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.119
r_sphericity_free26.358
r_rigid_bond_restr12.948
r_dihedral_angle_3_deg11.256
r_dihedral_angle_4_deg10.871
r_sphericity_bonded7.638
r_dihedral_angle_1_deg6.149
r_angle_other_deg3.547
r_long_range_B_refined2.918
r_long_range_B_other2.747
r_scangle_other2.267
r_angle_refined_deg1.938
r_scbond_it1.837
r_scbond_other1.837
r_mcangle_other1.515
r_mcangle_it1.514
r_mcbond_other1.149
r_mcbond_it1.148
r_chiral_restr0.382
r_bond_refined_d0.017
r_gen_planes_other0.016
r_gen_planes_refined0.011
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2506
Nucleic Acid Atoms
Solvent Atoms328
Heterogen Atoms111

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
MOLREPphasing