5ETN

E. coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.40 angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.55293Protein 6.6 mg/mL, 1 mM AMPCPP, 1 mM inhibitor, 2 mM magnesium chloride, 22%w/v PEG4000, 0.1 M sodium HEPES, 0.22 M calcium chloride
Crystal Properties
Matthews coefficientSolvent content
1.9837.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.88α = 90
b = 57.89β = 115.12
c = 38.61γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.9537Australian 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
11.434.9699.80.1119.3728184
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)
11.41.4299.90.6782.67

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 REPLACEMENTTHROUGHOUT5ETK1.434.9626803135699.790.184210.182310.21898RANDOM12.657
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]
0.160.26-0.25-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.066
r_sphericity_free25.609
r_dihedral_angle_4_deg21.438
r_rigid_bond_restr14.369
r_dihedral_angle_3_deg12.069
r_sphericity_bonded7.946
r_dihedral_angle_1_deg6.915
r_long_range_B_refined3.965
r_scangle_other3.769
r_long_range_B_other3.758
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.066
r_sphericity_free25.609
r_dihedral_angle_4_deg21.438
r_rigid_bond_restr14.369
r_dihedral_angle_3_deg12.069
r_sphericity_bonded7.946
r_dihedral_angle_1_deg6.915
r_long_range_B_refined3.965
r_scangle_other3.769
r_long_range_B_other3.758
r_angle_other_deg3.698
r_scbond_it3.592
r_scbond_other3.577
r_mcangle_it2.579
r_mcangle_other2.578
r_angle_refined_deg2.503
r_mcbond_it2.306
r_mcbond_other2.157
r_chiral_restr0.176
r_bond_refined_d0.041
r_gen_planes_other0.038
r_gen_planes_refined0.013
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 Atoms1275
Nucleic Acid Atoms
Solvent Atoms123
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
Cootmodel building
XDSdata reduction
MOLREPphasing
Aimlessdata scaling