2QGA

Plasmodium vivax adenylosuccinate lyase Pv003765 with AMP bound


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62982M Ammonia Sulfate, 0.2M K/Na Tartrate, 0.1M Na Citrate pH5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.3763.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.247α = 90
b = 179.545β = 99.37
c = 68.575γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2007-06-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.015099.90.10213.483.79333893338
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.012.0899.90.542.33.59285

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2hvg2.0133.838864788647468699.820.176930.17520.21013RANDOM28.845
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]
0.04-0.08-1.111.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.723
r_dihedral_angle_3_deg13.468
r_dihedral_angle_4_deg13.081
r_dihedral_angle_1_deg6.293
r_scangle_it3.626
r_scbond_it2.428
r_angle_refined_deg1.531
r_mcangle_it1.499
r_mcbond_it0.959
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.723
r_dihedral_angle_3_deg13.468
r_dihedral_angle_4_deg13.081
r_dihedral_angle_1_deg6.293
r_scangle_it3.626
r_scbond_it2.428
r_angle_refined_deg1.531
r_mcangle_it1.499
r_mcbond_it0.959
r_nbtor_refined0.3
r_symmetry_vdw_refined0.228
r_nbd_refined0.205
r_symmetry_hbond_refined0.188
r_xyhbond_nbd_refined0.167
r_chiral_restr0.107
r_symmetry_metal_ion_refined0.05
r_metal_ion_refined0.047
r_bond_refined_d0.017
r_gen_planes_refined0.007
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_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7297
Nucleic Acid Atoms
Solvent Atoms833
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing