5ETK

E. coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.09 angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Q0N 

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, 0.16 M CaCl2
Crystal Properties
Matthews coefficientSolvent content
1.9637.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.79α = 90
b = 57.69β = 115.57
c = 38.45γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-02-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.9707Australian 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
11.0934.6897.70.073147.257389
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)
11.091.11950.5633.16.7

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 REPLACEMENTTHROUGHOUT1Q0N1.0934.6854545283097.70.116720.115710.1364RANDOM10.46
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]
-0.04-0.09-0.270.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.17
r_sphericity_free27.331
r_dihedral_angle_4_deg17.576
r_rigid_bond_restr16.009
r_dihedral_angle_3_deg9.744
r_sphericity_bonded7.288
r_dihedral_angle_1_deg6.656
r_angle_other_deg3.54
r_long_range_B_refined3.091
r_long_range_B_other2.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.17
r_sphericity_free27.331
r_dihedral_angle_4_deg17.576
r_rigid_bond_restr16.009
r_dihedral_angle_3_deg9.744
r_sphericity_bonded7.288
r_dihedral_angle_1_deg6.656
r_angle_other_deg3.54
r_long_range_B_refined3.091
r_long_range_B_other2.67
r_scangle_other2.194
r_angle_refined_deg1.983
r_scbond_it1.885
r_scbond_other1.775
r_mcangle_it1.595
r_mcangle_other1.594
r_mcbond_it1.173
r_mcbond_other1.101
r_chiral_restr0.381
r_bond_refined_d0.028
r_gen_planes_other0.017
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 Atoms1275
Nucleic Acid Atoms
Solvent Atoms159
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
Cootmodel building
Aimlessdata scaling
XDSdata reduction
MOLREPphasing