3PJ2 | pdb_00003pj2

Crystal structure of BTK kinase domain complexed with 2-[4-(2-Diethylamino-ethoxy)-phenylamino]-6-(4-fluoro-phenoxy)-8-methyl-8H-pyrido[2,3-d]pyrimidin-7-one


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3PIXPDB ENTRY 3PIX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829333% PEG3350, 0.1M HEPES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2344.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.356α = 90
b = 104.803β = 90
c = 38.002γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.9795SSRLBL9-2

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
11.755092.70.06715.63.927449
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)
1.751.81600.2352.42.21560

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 3PIX1.7542.2226007139492.660.230860.229160.230.263070.26RANDOM33.022
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]
1.950.44-2.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.039
r_dihedral_angle_4_deg16.917
r_dihedral_angle_3_deg12.515
r_dihedral_angle_1_deg4.638
r_scangle_it1.671
r_scbond_it1.048
r_angle_refined_deg0.959
r_mcangle_it0.887
r_mcbond_it0.542
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.039
r_dihedral_angle_4_deg16.917
r_dihedral_angle_3_deg12.515
r_dihedral_angle_1_deg4.638
r_scangle_it1.671
r_scbond_it1.048
r_angle_refined_deg0.959
r_mcangle_it0.887
r_mcbond_it0.542
r_nbtor_refined0.304
r_nbd_refined0.175
r_symmetry_vdw_refined0.166
r_xyhbond_nbd_refined0.097
r_symmetry_hbond_refined0.095
r_chiral_restr0.069
r_bond_refined_d0.006
r_gen_planes_refined0.003
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 Atoms2041
Nucleic Acid Atoms
Solvent Atoms142
Heterogen Atoms35

Software

Software
Software NamePurpose
ADSCdata collection
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing