3FZP

Crystal structure of PYK2 complexed with ATPgS


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52980.1M Citrate, 0.5-1.5M Lithium Sulfate, 0.2-0.4M Ammonium Sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2745.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.946α = 90
b = 92.663β = 92.45
c = 42.671γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 2102007-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-IDAPS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.13094.10.0418.42.315837
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.12.1890.50.242.72.21527

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2.1301498980294.060.212270.210710.23898RANDOM47.727
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]
-0.19-0.77-1.581.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.202
r_dihedral_angle_4_deg19.604
r_dihedral_angle_3_deg18.547
r_dihedral_angle_1_deg7.007
r_scangle_it3.455
r_scbond_it2.248
r_mcangle_it1.726
r_angle_refined_deg1.713
r_mcbond_it1.05
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.202
r_dihedral_angle_4_deg19.604
r_dihedral_angle_3_deg18.547
r_dihedral_angle_1_deg7.007
r_scangle_it3.455
r_scbond_it2.248
r_mcangle_it1.726
r_angle_refined_deg1.713
r_mcbond_it1.05
r_nbtor_refined0.313
r_symmetry_hbond_refined0.252
r_nbd_refined0.221
r_symmetry_vdw_refined0.22
r_xyhbond_nbd_refined0.205
r_chiral_restr0.147
r_bond_refined_d0.015
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_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 Atoms2098
Nucleic Acid Atoms
Solvent Atoms105
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement