3CS9

Human ABL kinase in complex with nilotinib


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529810.5 % PEG 5000 MME, 0.1 M MES pH 5.5, 0.05 ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6854.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.926α = 90
b = 118.088β = 90
c = 123.683γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2004-01-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.00033SLSX06SA

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
12.24098.580.0567.536894268942
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)
2.22.2897.10.4016.256728

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTUnpublished structure of Abl complex2.21406540665406347798.580.199650.199650.197440.24186RANDOM46.122
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]
0.020.58-0.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.392
r_dihedral_angle_4_deg15.827
r_dihedral_angle_3_deg15.245
r_dihedral_angle_1_deg6.544
r_scangle_it3.245
r_scbond_it2.297
r_mcangle_it1.664
r_angle_refined_deg1.594
r_mcbond_it1.217
r_angle_other_deg1.035
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.392
r_dihedral_angle_4_deg15.827
r_dihedral_angle_3_deg15.245
r_dihedral_angle_1_deg6.544
r_scangle_it3.245
r_scbond_it2.297
r_mcangle_it1.664
r_angle_refined_deg1.594
r_mcbond_it1.217
r_angle_other_deg1.035
r_symmetry_vdw_other0.256
r_symmetry_hbond_refined0.24
r_mcbond_other0.236
r_symmetry_vdw_refined0.233
r_nbd_refined0.215
r_nbd_other0.19
r_xyhbond_nbd_refined0.17
r_chiral_restr0.092
r_nbtor_other0.092
r_bond_refined_d0.019
r_gen_planes_other0.01
r_gen_planes_refined0.008
r_bond_other_d0.002
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8274
Nucleic Acid Atoms
Solvent Atoms266
Heterogen Atoms156

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing