1ZN8

Human Adenine Phosphoribosyltransferase Complexed with AMP, in Space Group P1 at 1.76 A Resolution


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 , VAPOR DIFFUSION, HANGING DROP, temperature 291 K, pH 8.50
Crystal Properties
Matthews coefficientSolvent content
2.1742.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.06α = 75.41
b = 47.47β = 68.42
c = 47.84γ = 61.49
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayIMAGE PLATEMARRESEARCHMSINGLE WAVELENGTH
21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418
2SYNCHROTRONLNLS BEAMLINE D03B-MX11.4538LNLSD03B-MX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.764431837

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 REPLACEMENTTHROUGHOUT1.764430208162995.50.160.1570.211RANDOM17.51
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]
-0.480.96-0.34-0.37-0.240.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.747
r_dihedral_angle_4_deg22.271
r_dihedral_angle_3_deg15.397
r_dihedral_angle_1_deg6.317
r_scangle_it4.006
r_scbond_it2.758
r_angle_refined_deg1.932
r_mcangle_it1.607
r_mcbond_it1.467
r_angle_other_deg0.962
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.747
r_dihedral_angle_4_deg22.271
r_dihedral_angle_3_deg15.397
r_dihedral_angle_1_deg6.317
r_scangle_it4.006
r_scbond_it2.758
r_angle_refined_deg1.932
r_mcangle_it1.607
r_mcbond_it1.467
r_angle_other_deg0.962
r_mcbond_other0.3
r_symmetry_vdw_other0.295
r_symmetry_vdw_refined0.284
r_xyhbond_nbd_refined0.23
r_symmetry_hbond_refined0.219
r_nbd_refined0.214
r_nbd_other0.203
r_nbtor_refined0.18
r_chiral_restr0.133
r_nbtor_other0.088
r_bond_refined_d0.02
r_bond_other_d0.007
r_gen_planes_refined0.007
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
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 Atoms2717
Nucleic Acid Atoms
Solvent Atoms355
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement