3LGD

Crystal structure of human adenosine deaminase growth factor, adenosine deaminase type 2 (ADA2)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.0429340% MPD, 5% PEG 8000, 0.1M cacodylate, pH 6.04, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8857.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.212α = 113.38
b = 73.099β = 94.18
c = 80.662γ = 92.16
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2007-06-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.90ESRFID29

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
11.97397.40.10.18.82.110121522.389
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)
1.9296.90.430.4311.92.231991

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 DIFFRACTIONSADTHROUGHOUT239.6882592427697.470.187050.184610.23397RANDOM27.935
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]
-0.11-0.22-0.160.06-0.27-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.04
r_dihedral_angle_4_deg18.139
r_dihedral_angle_3_deg16.12
r_dihedral_angle_1_deg5.803
r_scangle_it3.778
r_scbond_it2.356
r_angle_refined_deg1.379
r_mcangle_it1.353
r_mcbond_it0.718
r_chiral_restr0.104
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.04
r_dihedral_angle_4_deg18.139
r_dihedral_angle_3_deg16.12
r_dihedral_angle_1_deg5.803
r_scangle_it3.778
r_scbond_it2.356
r_angle_refined_deg1.379
r_mcangle_it1.353
r_mcbond_it0.718
r_chiral_restr0.104
r_bond_refined_d0.014
r_gen_planes_refined0.006
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 Atoms7858
Nucleic Acid Atoms
Solvent Atoms789
Heterogen Atoms96

Software

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