5ETV

S. aureus 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.72 angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4CWB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293Protein 6.9 mg/mL, 1 mM AMPCPP, 1 mM inhibitor, 2 mM magnesium chloride,0.186 M sodium nitrate, 18.4%w/v PEG3000, 50 mM sodium thiocyanate
Crystal Properties
Matthews coefficientSolvent content
2.9358.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.25α = 90
b = 84.25β = 90
c = 52.411γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-06-09MSINGLE 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
11.7242.571000.12420.320.222673
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)
11.721.751000.959520.1

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 REPLACEMENTTHROUGHOUT4CWB1.7242.5721515113199.980.181810.180520.20717RANDOM12.834
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]
0.30.150.3-0.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.288
r_dihedral_angle_4_deg15.389
r_dihedral_angle_3_deg10.639
r_dihedral_angle_1_deg6.466
r_long_range_B_refined5.727
r_long_range_B_other5.52
r_scangle_other3.755
r_angle_other_deg3.551
r_scbond_it2.507
r_scbond_other2.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.288
r_dihedral_angle_4_deg15.389
r_dihedral_angle_3_deg10.639
r_dihedral_angle_1_deg6.466
r_long_range_B_refined5.727
r_long_range_B_other5.52
r_scangle_other3.755
r_angle_other_deg3.551
r_scbond_it2.507
r_scbond_other2.48
r_angle_refined_deg1.853
r_mcangle_other1.642
r_mcangle_it1.634
r_mcbond_it1.111
r_mcbond_other1.063
r_chiral_restr0.107
r_bond_refined_d0.013
r_gen_planes_other0.013
r_gen_planes_refined0.008
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 Atoms1264
Nucleic Acid Atoms
Solvent Atoms101
Heterogen Atoms59

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Cootmodel building
Aimlessdata scaling
MOLREPphasing