2AMX

Crystal structure of Plasmodium Yoelii Adenosine deaminase (PY02076)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.530020% PEG 3350, 0.1 M Na cacodylate pH 5.5, 0.2 M MgCl2, 10 mM CoCl2, VAPOR DIFFUSION, temperature 300 K, pH 5.50
Crystal Properties
Matthews coefficientSolvent content
2.550.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.719α = 90
b = 90.332β = 90
c = 137.086γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVVERIMAX2005-07-14MSINGLE WAVELENGTH
21x-rayMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E

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
2,12.0242.999.70.1030.1037.25.65510855046
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)
2.022.0599.10.6990.6992.135.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.0242.9541325413277399.70.1970.1960.246RANDOM26.6
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]
-0.020.34-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.063
r_dihedral_angle_4_deg22.944
r_dihedral_angle_3_deg16.304
r_dihedral_angle_1_deg6.549
r_scangle_it3.839
r_scbond_it2.579
r_mcangle_it1.697
r_angle_refined_deg1.686
r_mcbond_it1.038
r_metal_ion_refined0.362
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.063
r_dihedral_angle_4_deg22.944
r_dihedral_angle_3_deg16.304
r_dihedral_angle_1_deg6.549
r_scangle_it3.839
r_scbond_it2.579
r_mcangle_it1.697
r_angle_refined_deg1.686
r_mcbond_it1.038
r_metal_ion_refined0.362
r_symmetry_hbond_refined0.327
r_symmetry_vdw_refined0.326
r_nbtor_refined0.306
r_nbd_refined0.205
r_xyhbond_nbd_refined0.173
r_chiral_restr0.111
r_bond_refined_d0.02
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms5866
Nucleic Acid Atoms
Solvent Atoms495
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
HKL-2000data scaling
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building