4RFY | pdb_00004rfy

Crystal structure of BTK kinase domain complexed with 6-(dimethylamino)-2-[2-(hydroxymethyl)-3-[1-methyl-5-[[5-(morpholine-4-carbonyl)-2-pyridyl]amino]-6-oxo-3-pyridyl]phenyl]-3,4-dihydroisoquinolin-1-one


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4OTRPDB ENTRY 4OTR

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
2.2645.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.805α = 90
b = 107.123β = 90
c = 38.305γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.0ALS5.0.2

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
11.75098.40.11411.1533099
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)
11.71.7495.30.5524.2

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 4OTR1.742.9131214166298.550.183860.182050.180.218820.22RANDOM24.365
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]
2.330.49-2.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.943
r_dihedral_angle_4_deg17.588
r_dihedral_angle_3_deg12.49
r_long_range_B_refined6.234
r_dihedral_angle_1_deg6.181
r_scbond_it2.767
r_mcangle_it2.013
r_angle_refined_deg1.927
r_mcbond_it1.416
r_chiral_restr0.155
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.943
r_dihedral_angle_4_deg17.588
r_dihedral_angle_3_deg12.49
r_long_range_B_refined6.234
r_dihedral_angle_1_deg6.181
r_scbond_it2.767
r_mcangle_it2.013
r_angle_refined_deg1.927
r_mcbond_it1.416
r_chiral_restr0.155
r_bond_refined_d0.022
r_gen_planes_refined0.013
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2139
Nucleic Acid Atoms
Solvent Atoms250
Heterogen Atoms53

Software

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