5U99

Transition state analysis of adenosine triphosphate phosphoribosyltransferase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NH7PDB:1NH7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293.151.6 M magnesium sulphate and 0.1 M, 2-(N-morpholino)ethanesulfonic acid
Crystal Properties
Matthews coefficientSolvent content
3.1661.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.758α = 90
b = 134.758β = 90
c = 111.005γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2015-03-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.9537Australian SynchrotronMX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
12.480.431000.1430.4920.773202015289

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 REPLACEMENTTHROUGHOUTPDB:1NH72.480.431454074799.960.217490.215710.25051RANDOM55.545
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]
1.640.821.64-5.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.637
r_dihedral_angle_4_deg21.034
r_dihedral_angle_3_deg14.881
r_dihedral_angle_1_deg6.929
r_long_range_B_refined4.401
r_long_range_B_other4.389
r_scangle_other2.063
r_mcangle_it1.98
r_mcangle_other1.979
r_angle_refined_deg1.519
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.637
r_dihedral_angle_4_deg21.034
r_dihedral_angle_3_deg14.881
r_dihedral_angle_1_deg6.929
r_long_range_B_refined4.401
r_long_range_B_other4.389
r_scangle_other2.063
r_mcangle_it1.98
r_mcangle_other1.979
r_angle_refined_deg1.519
r_scbond_it1.303
r_scbond_other1.302
r_mcbond_it1.141
r_mcbond_other1.141
r_angle_other_deg0.958
r_chiral_restr0.08
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms1981
Nucleic Acid Atoms
Solvent Atoms28
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing