4RFZ | pdb_00004rfz

Crystal structure of BTK kinase domain complexed with 6-(dimethylamino)-8-fluoro-2-[2-(hydroxymethyl)-3-[1-methyl-5-[[5-(morpholine-4-carbonyl)-2-pyridyl]amino]-6-oxo-3-pyridyl]phenyl]isoquinolin-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
2.2445.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.936α = 90
b = 106.197β = 90
c = 38.22γ = 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
11.175087.50.04621.84.88647010.6
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)
11.171.2138.10.4321.82.8

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 4OTR1.1742.7282059434487.110.157910.156590.160.183570.18RANDOM18.282
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]
0.82-0.31-0.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.935
r_sphericity_free24.834
r_dihedral_angle_4_deg14.687
r_dihedral_angle_3_deg11.52
r_sphericity_bonded9.463
r_rigid_bond_restr8.572
r_dihedral_angle_1_deg5.972
r_long_range_B_refined3.552
r_scbond_it3.287
r_mcangle_it2.105
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.935
r_sphericity_free24.834
r_dihedral_angle_4_deg14.687
r_dihedral_angle_3_deg11.52
r_sphericity_bonded9.463
r_rigid_bond_restr8.572
r_dihedral_angle_1_deg5.972
r_long_range_B_refined3.552
r_scbond_it3.287
r_mcangle_it2.105
r_angle_refined_deg1.983
r_mcbond_it1.774
r_chiral_restr0.137
r_bond_refined_d0.021
r_gen_planes_refined0.014
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 Atoms294
Heterogen Atoms54

Software

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