4OTQ

Crystal structure of BTK kinase domain complexed with 1-[5-[3-(7-tert-butyl-4-oxo-quinazolin-3-yl)-2-methyl-phenyl]-1-methyl-2-oxo-3-pyridyl]-3-methyl-urea


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, 0.1 M HEPES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2645.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.886α = 90
b = 106.562β = 90
c = 38.304γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.97946SSRLBL9-2

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
11.5542.899.50.06717.64.74360421.7
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)
11.551.5999.640.4132.34.12667

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 3PIX1.5542.841259219199.640.150220.148080.18882RANDOM25.359
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]
-0.060.63-0.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.289
r_sphericity_free22.269
r_dihedral_angle_4_deg15.479
r_dihedral_angle_3_deg10.984
r_sphericity_bonded10.69
r_rigid_bond_restr7.015
r_dihedral_angle_1_deg5.836
r_long_range_B_refined4.48
r_scbond_it3.637
r_mcangle_it2.846
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.289
r_sphericity_free22.269
r_dihedral_angle_4_deg15.479
r_dihedral_angle_3_deg10.984
r_sphericity_bonded10.69
r_rigid_bond_restr7.015
r_dihedral_angle_1_deg5.836
r_long_range_B_refined4.48
r_scbond_it3.637
r_mcangle_it2.846
r_mcbond_it2.496
r_angle_refined_deg1.728
r_chiral_restr0.148
r_bond_refined_d0.02
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2139
Nucleic Acid Atoms
Solvent Atoms259
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing