5ETP

E. coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.05 angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9.1281PROTEIN 6.6 MG/ML 1 MM AMPCPP, 1 MM INHIBITOR, 2 MM MAGNESIUM CHLORIDE, 20%w/v PEG4000, 0.1 M TRIS CHLORIDE, 0.172 M CALCIUM CHLORIDE
Crystal Properties
Matthews coefficientSolvent content
1.9737.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.95α = 90
b = 57.77β = 116.11
c = 38.64γ = 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
11.0534.799.80.08713.47.166451
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)
11.051.0699.20.2985.16.5

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 REPLACEMENTTHROUGHOUT1Q0N1.0534.763260316299.720.107910.107060.12504RANDOM6.66
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]
-0.070.050.06-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.606
r_sphericity_free20.21
r_dihedral_angle_4_deg16.169
r_rigid_bond_restr12.398
r_dihedral_angle_3_deg10.271
r_dihedral_angle_1_deg6.346
r_sphericity_bonded4.797
r_angle_other_deg3.529
r_long_range_B_refined2.407
r_long_range_B_other2.406
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.606
r_sphericity_free20.21
r_dihedral_angle_4_deg16.169
r_rigid_bond_restr12.398
r_dihedral_angle_3_deg10.271
r_dihedral_angle_1_deg6.346
r_sphericity_bonded4.797
r_angle_other_deg3.529
r_long_range_B_refined2.407
r_long_range_B_other2.406
r_angle_refined_deg2.099
r_scangle_other1.196
r_scbond_it0.931
r_scbond_other0.931
r_mcangle_it0.829
r_mcangle_other0.829
r_mcbond_it0.625
r_mcbond_other0.625
r_chiral_restr0.116
r_gen_planes_other0.022
r_bond_refined_d0.019
r_gen_planes_refined0.014
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 Atoms1280
Nucleic Acid Atoms
Solvent Atoms282
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
MOLREPphasing
XDSdata reduction
Cootmodel building