5ETQ

S. aureus 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and inhibitor at 1.96 angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5281PROTEIN 6.9 MG/ML, 1 MM AMPCPP, 1 MM INHIBITOR, 0.202 M MAGNESIUM CHLORIDE, 0.1 M TRIS CHLORIDE, 20%w/v PEG8000, 50 MM SODIUM THIOCYANATE
Crystal Properties
Matthews coefficientSolvent content
2.2545.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.63α = 90
b = 68.2β = 106.05
c = 52.82γ = 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
11.9668.21000.1179.1723517
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)
11.962.0199.80.4973.26.6

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 REPLACEMENTTHROUGHOUT4CWB1.9650.7622352114699.940.183840.182190.21566RANDOM12.433
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]
-0.19-0.922.16-1.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.713
r_dihedral_angle_4_deg12.936
r_dihedral_angle_3_deg11.845
r_dihedral_angle_1_deg6.36
r_long_range_B_refined6.351
r_long_range_B_other6.351
r_scangle_other5.092
r_angle_other_deg3.613
r_scbond_it3.499
r_scbond_other3.497
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.713
r_dihedral_angle_4_deg12.936
r_dihedral_angle_3_deg11.845
r_dihedral_angle_1_deg6.36
r_long_range_B_refined6.351
r_long_range_B_other6.351
r_scangle_other5.092
r_angle_other_deg3.613
r_scbond_it3.499
r_scbond_other3.497
r_mcangle_other2.212
r_mcangle_it2.204
r_angle_refined_deg1.884
r_mcbond_it1.571
r_mcbond_other1.553
r_chiral_restr0.252
r_bond_refined_d0.012
r_gen_planes_other0.009
r_gen_planes_refined0.007
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 Atoms2508
Nucleic Acid Atoms
Solvent Atoms136
Heterogen Atoms111

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
Cootmodel building