5ETO

E. coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.07 angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.88293PROTEIN 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 CACL2
Crystal Properties
Matthews coefficientSolvent content
1.9637.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.77α = 90
b = 57.75β = 115.46
c = 38.42γ = 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
11.0734.6998.60.09710.17.161436
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)
11.071.0996.80.81926.7

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 REPLACEMENTTHROUGHOUT5ETK1.0734.6958452297098.650.129940.128970.14996RANDOM10.24
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]
-0.11-0.20.010.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.455
r_sphericity_free29.392
r_dihedral_angle_4_deg18.644
r_rigid_bond_restr17.274
r_dihedral_angle_3_deg9.832
r_sphericity_bonded7.208
r_dihedral_angle_1_deg6.879
r_angle_other_deg3.544
r_long_range_B_refined3.124
r_long_range_B_other2.721
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.455
r_sphericity_free29.392
r_dihedral_angle_4_deg18.644
r_rigid_bond_restr17.274
r_dihedral_angle_3_deg9.832
r_sphericity_bonded7.208
r_dihedral_angle_1_deg6.879
r_angle_other_deg3.544
r_long_range_B_refined3.124
r_long_range_B_other2.721
r_scangle_other2.049
r_angle_refined_deg1.968
r_scbond_it1.557
r_scbond_other1.557
r_mcangle_it1.525
r_mcangle_other1.525
r_mcbond_it1.09
r_mcbond_other1.09
r_chiral_restr0.116
r_bond_refined_d0.019
r_gen_planes_other0.018
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 Atoms1272
Nucleic Acid Atoms
Solvent Atoms151
Heterogen Atoms59

Software

Software
Software NamePurpose
REFMACrefinement
Cootmodel building
Aimlessdata scaling
MOLREPphasing
XDSdata reduction