3ET7

Crystal structure of PYK2 complexed with PF-2318841


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSIONVAPOR DIFFUSION
Crystal Properties
Matthews coefficientSolvent content
3.3363.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.824α = 90
b = 106.824β = 90
c = 75.185γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.542

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
12.73097.70.0710.0717.21218312183
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)
2.72.898.80.7640.7642.96.81198

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2.730121831159658797.860.250680.250680.246640.3283RANDOM61.703
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]
-1.13-1.132.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg11.769
r_scangle_it5.696
r_scbond_it3.576
r_angle_refined_deg2.973
r_mcangle_it2.675
r_mcbond_it1.448
r_symmetry_hbond_refined0.431
r_symmetry_vdw_refined0.329
r_nbd_refined0.328
r_xyhbond_nbd_refined0.246
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg11.769
r_scangle_it5.696
r_scbond_it3.576
r_angle_refined_deg2.973
r_mcangle_it2.675
r_mcbond_it1.448
r_symmetry_hbond_refined0.431
r_symmetry_vdw_refined0.329
r_nbd_refined0.328
r_xyhbond_nbd_refined0.246
r_chiral_restr0.18
r_bond_refined_d0.032
r_gen_planes_refined0.012
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
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 Atoms2114
Nucleic Acid Atoms
Solvent Atoms12
Heterogen Atoms42

Software

Software
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling