5ETM

E. coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.46 angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.55293Protein 6.6 mg/mL, 1 mM AMPCPP, 1 mM inhibitor, 2 mM Magnesium Chloride, 27.5 %w/v PEG4000, 0.1 M sodium HEPES, 0.196 M Calcium Chloride
Crystal Properties
Matthews coefficientSolvent content
1.9536.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.763α = 90
b = 57.631β = 115.49
c = 38.407γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-09-26MSINGLE 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
11.4634.6799.80.09711.67.124472
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)
11.461.4899.90.6622.76.5

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 REPLACEMENTTHROUGHOUT5ETK1.4634.6723060139199.760.20630.204410.23939RANDOM12.946
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]
0.48-0.42-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.376
r_dihedral_angle_4_deg17.167
r_dihedral_angle_3_deg11.552
r_dihedral_angle_1_deg6.733
r_long_range_B_refined4.291
r_long_range_B_other4.245
r_angle_other_deg3.558
r_scangle_other2.781
r_angle_refined_deg2.206
r_mcangle_it2.046
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.376
r_dihedral_angle_4_deg17.167
r_dihedral_angle_3_deg11.552
r_dihedral_angle_1_deg6.733
r_long_range_B_refined4.291
r_long_range_B_other4.245
r_angle_other_deg3.558
r_scangle_other2.781
r_angle_refined_deg2.206
r_mcangle_it2.046
r_mcangle_other2.045
r_scbond_other1.891
r_scbond_it1.862
r_mcbond_it1.358
r_mcbond_other1.358
r_chiral_restr0.128
r_bond_refined_d0.021
r_gen_planes_other0.02
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1275
Nucleic Acid Atoms
Solvent Atoms88
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement
Cootmodel building
Aimlessdata scaling
XDSdata reduction
MOLREPphasing