3LGG

Crystal structure of human adenosine deaminase growth factor, adenosine deaminase type 2 (ADA2) complexed with transition state analogue, coformycin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.0429340% MPD, 5% PEG 8000, 0.1M cacodylate, 2 mM coformycin, pH 6.04, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8757.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.249α = 113.55
b = 72.993β = 94.89
c = 80.537γ = 91.53
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2007-06-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.009ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.573.5296.80.0690.0699.7943.94396740.899
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.52.6495.80.320.323.13.96368

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 DIFFRACTIONSADTHROUGHOUT2.566.8241746222196.840.194140.192490.22483RANDOM34.931
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]
-0.1-0.4-0.120.18-0.46-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.397
r_dihedral_angle_3_deg18.085
r_dihedral_angle_4_deg17.321
r_dihedral_angle_1_deg5.292
r_scangle_it2.724
r_scbond_it1.531
r_angle_refined_deg1.225
r_mcangle_it0.965
r_mcbond_it0.474
r_chiral_restr0.079
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.397
r_dihedral_angle_3_deg18.085
r_dihedral_angle_4_deg17.321
r_dihedral_angle_1_deg5.292
r_scangle_it2.724
r_scbond_it1.531
r_angle_refined_deg1.225
r_mcangle_it0.965
r_mcbond_it0.474
r_chiral_restr0.079
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7855
Nucleic Acid Atoms
Solvent Atoms244
Heterogen Atoms126

Software

Software
Software NamePurpose
DNAdata collection
PHENIXmodel building
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing