1ZN7

Human Adenine Phosphoribosyltransferase Complexed with PRPP, ADE and R5P


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529115.0 % (V/V) glycerol, 25.5 % (w/V) polyethylene glycol 4000, 0.17 mol/L sodium acetate and 0.085 mol/L Tris-HCl pH 8.5, temperature 291K, VAPOR DIFFUSION, HANGING DROP, pH 8.50
Crystal Properties
Matthews coefficientSolvent content
2.1141.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.019α = 76.59
b = 47.267β = 69.26
c = 47.522γ = 61.89
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayIMAGE PLATEMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
11.8339.75960.069928504
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)
11.831.9393.50.3871.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.8339.7527055144897.20.1480.1460.19RANDOM18
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]
-0.141.41-0.83-0.970.260.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.838
r_dihedral_angle_4_deg20.455
r_dihedral_angle_3_deg15.151
r_dihedral_angle_1_deg6.446
r_scangle_it3.528
r_scbond_it2.407
r_angle_refined_deg1.815
r_mcangle_it1.473
r_mcbond_it1.03
r_angle_other_deg0.965
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.838
r_dihedral_angle_4_deg20.455
r_dihedral_angle_3_deg15.151
r_dihedral_angle_1_deg6.446
r_scangle_it3.528
r_scbond_it2.407
r_angle_refined_deg1.815
r_mcangle_it1.473
r_mcbond_it1.03
r_angle_other_deg0.965
r_mcbond_other0.287
r_symmetry_vdw_other0.257
r_symmetry_hbond_refined0.232
r_nbd_refined0.217
r_xyhbond_nbd_refined0.211
r_nbd_other0.204
r_nbtor_refined0.168
r_symmetry_vdw_refined0.131
r_chiral_restr0.112
r_metal_ion_refined0.094
r_nbtor_other0.085
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2715
Nucleic Acid Atoms
Solvent Atoms367
Heterogen Atoms104

Software

Software
Software NamePurpose
REFMACrefinement