3QRI

The crystal structure of human abl1 kinase domain in complex with DCC-2036


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherAbl kinase

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.229032% PEG 3000, 100MM TRIS PH 8.2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties
Matthews coefficientSolvent content
2.1141.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.26α = 90
b = 59.7β = 108.71
c = 79.43γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-06-07MSINGLE 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
12.17597.40.11413.1322653142616
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.284.12.6

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTAbl kinase2.157.08322653207415400.2160.2160.2130.272RANDOM26.43
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]
1.320.85-10.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.285
r_dihedral_angle_3_deg12.154
r_dihedral_angle_4_deg12.014
r_dihedral_angle_1_deg4.599
r_scangle_it1.794
r_angle_refined_deg1.438
r_scbond_it1.087
r_mcangle_it0.9
r_angle_other_deg0.857
r_mcbond_it0.482
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.285
r_dihedral_angle_3_deg12.154
r_dihedral_angle_4_deg12.014
r_dihedral_angle_1_deg4.599
r_scangle_it1.794
r_angle_refined_deg1.438
r_scbond_it1.087
r_mcangle_it0.9
r_angle_other_deg0.857
r_mcbond_it0.482
r_chiral_restr0.077
r_mcbond_other0.067
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4329
Nucleic Acid Atoms
Solvent Atoms400
Heterogen Atoms84

Software

Software
Software NamePurpose
BOSdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling