6FD5

Crystal Structure of Human APRT-Tyr105Phe variant in complex with Adenine, PRPP and Mg2+, 14 days post crystallization (with AMP and PPi products partially generated)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293NAOAC, PEG4000, GLYCEROL, TRIS, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
Crystal Properties
Matthews coefficientSolvent content
2.346.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.232α = 77.3
b = 47.75β = 61.71
c = 48.039γ = 69.47
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2015-09-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.98ESRFID23-2

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
11.5544.6296.70.0798.73.548487
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)
11.551.5894.50.6613.6

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 REPLACEMENTTHROUGHOUT5HND1.5544.6246043244296.70.1760.1750.201RANDOM18.82
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]
0.22-0.120.46-0.08-0.490.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.734
r_dihedral_angle_4_deg18.981
r_dihedral_angle_3_deg12.218
r_dihedral_angle_1_deg6.08
r_mcangle_it1.845
r_mcbond_it1.343
r_mcbond_other1.342
r_angle_refined_deg1.298
r_angle_other_deg0.608
r_chiral_restr0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.734
r_dihedral_angle_4_deg18.981
r_dihedral_angle_3_deg12.218
r_dihedral_angle_1_deg6.08
r_mcangle_it1.845
r_mcbond_it1.343
r_mcbond_other1.342
r_angle_refined_deg1.298
r_angle_other_deg0.608
r_chiral_restr0.07
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d
r_gen_planes_other
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_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2638
Nucleic Acid Atoms
Solvent Atoms212
Heterogen Atoms94

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement