2AX4

Crystal structure of the kinase domain of human 3'-phosphoadenosine 5'-phosphosulphate synthetase 2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9.5298PEG3350 18%, 0.2M Ammonium Citrate, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.754.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.914α = 90
b = 131.892β = 104.58
c = 70.562γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2005-08-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54

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
12.55098.30.1213.143.53174911
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)
2.52.591000.3444.883.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.530130052160197.920.2150.211590.27835RANDOM15.764
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]
-0.230.22-0.921.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.41
r_dihedral_angle_4_deg18.522
r_dihedral_angle_3_deg18.446
r_dihedral_angle_1_deg6.086
r_scangle_it3.207
r_scbond_it1.998
r_angle_refined_deg1.668
r_mcangle_it1.219
r_mcbond_it0.706
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.41
r_dihedral_angle_4_deg18.522
r_dihedral_angle_3_deg18.446
r_dihedral_angle_1_deg6.086
r_scangle_it3.207
r_scbond_it1.998
r_angle_refined_deg1.668
r_mcangle_it1.219
r_mcbond_it0.706
r_nbtor_refined0.314
r_symmetry_vdw_refined0.227
r_nbd_refined0.223
r_xyhbond_nbd_refined0.172
r_symmetry_hbond_refined0.146
r_chiral_restr0.108
r_bond_refined_d0.015
r_gen_planes_refined0.006
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_refined
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 Atoms6128
Nucleic Acid Atoms
Solvent Atoms292
Heterogen Atoms108

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing