3OCT

Crystal structure of bruton's tyrosine kinase mutant V555R in complex with dasatinib


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OCS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.4289100 MM MES, PH 5.4, 20% PEG 3500, 200 MM NACL, 3% POLYPROPYLENE GLYCOL P 400, VAPOR DIFFUSION, TEMPERATURE 289K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.1843.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.101α = 90
b = 42.944β = 112.58
c = 64.542γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-02-08SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.98APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.7659.5581.50.07710.63.222490
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.761.82510.3642.2

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3OCS1.9559.55183799730.1990.1960.251RANDOM27.924
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]
2.42.86-0.990.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.501
r_dihedral_angle_4_deg16.764
r_dihedral_angle_3_deg14.96
r_dihedral_angle_1_deg6.443
r_scangle_it3.649
r_scbond_it2.368
r_angle_refined_deg1.543
r_mcangle_it1.401
r_mcbond_it0.742
r_chiral_restr0.102
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.501
r_dihedral_angle_4_deg16.764
r_dihedral_angle_3_deg14.96
r_dihedral_angle_1_deg6.443
r_scangle_it3.649
r_scbond_it2.368
r_angle_refined_deg1.543
r_mcangle_it1.401
r_mcbond_it0.742
r_chiral_restr0.102
r_bond_refined_d0.015
r_gen_planes_refined0.006
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1992
Nucleic Acid Atoms
Solvent Atoms101
Heterogen Atoms33

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement