3PJ3 | pdb_00003pj3

Crystal structure of BTK kinase domain complexed with 2-Methyl-5-[(E)-(3-phenyl-acryloyl)amino]-N-(2-phenyl-3H-imidazo[4,5-b]pyridin-6-yl)-benzamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 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
2.2645.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.614α = 90
b = 105.448β = 90
c = 38.121γ = 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
1SYNCHROTRONALS BEAMLINE 5.0.21.0000ALS5.0.2

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
11.8540950.1578.45.724080
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)
1.851.9263.10.7171.91.81560

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 SYNTHESISTHROUGHOUT3PIX1.8538.1222792122794.810.234240.233150.230.254480.25RANDOM31.319
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]
0.440.26-0.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.252
r_dihedral_angle_4_deg17.206
r_dihedral_angle_3_deg13.765
r_dihedral_angle_1_deg4.888
r_scangle_it1.807
r_scbond_it1.136
r_mcangle_it0.957
r_angle_refined_deg0.946
r_mcbond_it0.587
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.252
r_dihedral_angle_4_deg17.206
r_dihedral_angle_3_deg13.765
r_dihedral_angle_1_deg4.888
r_scangle_it1.807
r_scbond_it1.136
r_mcangle_it0.957
r_angle_refined_deg0.946
r_mcbond_it0.587
r_nbtor_refined0.301
r_symmetry_vdw_refined0.184
r_nbd_refined0.177
r_symmetry_hbond_refined0.129
r_xyhbond_nbd_refined0.104
r_chiral_restr0.07
r_bond_refined_d0.007
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 Atoms1979
Nucleic Acid Atoms
Solvent Atoms96
Heterogen Atoms36

Software

Software
Software NamePurpose
ADSCdata collection
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing