6HGP

Crystal Structure of Human APRT wild type in complex with Phosphate ion.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6FCH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293NaOAc, PEG4000, Glycerol, Tris
Crystal Properties
Matthews coefficientSolvent content
2.2845.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.41α = 77.07
b = 47.6β = 69.39
c = 47.66γ = 61.69
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2014-10-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.9785SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.744.594.80.070.9866.12.235712
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)
11.71.7394.20.3361.72.2

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 REPLACEMENTTHROUGHOUT6FCH1.744.533932177994.830.18350.18230.205RANDOM24.333
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]
-0.030.53-0.41-0.240.120.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.824
r_dihedral_angle_4_deg22.12
r_dihedral_angle_3_deg13.986
r_dihedral_angle_1_deg6.062
r_mcangle_it2.69
r_mcbond_it2.037
r_mcbond_other2.026
r_angle_refined_deg1.083
r_angle_other_deg0.576
r_chiral_restr0.071
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.824
r_dihedral_angle_4_deg22.12
r_dihedral_angle_3_deg13.986
r_dihedral_angle_1_deg6.062
r_mcangle_it2.69
r_mcbond_it2.037
r_mcbond_other2.026
r_angle_refined_deg1.083
r_angle_other_deg0.576
r_chiral_restr0.071
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2663
Nucleic Acid Atoms
Solvent Atoms138
Heterogen Atoms10

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing