4BKJ

Crystal structure of the human DDR1 kinase domain in complex with imatinib


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1M BIS-TRIS PH 6.3, 34% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.2846.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.074α = 90
b = 60.074β = 90
c = 180.575γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

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
11.745.1499.90.0813.56.5728472
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)
11.71.7399.70.632.96.5

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3ZOS1.745.1469069369099.910.156560.155540.17556RANDOM25.117
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]
-2.2-17.4919.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.424
r_dihedral_angle_4_deg14.332
r_dihedral_angle_3_deg11.891
r_dihedral_angle_1_deg5.19
r_scbond_it2.248
r_mcangle_it2.075
r_mcbond_it1.478
r_mcbond_other1.478
r_angle_refined_deg1.235
r_angle_other_deg0.886
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.424
r_dihedral_angle_4_deg14.332
r_dihedral_angle_3_deg11.891
r_dihedral_angle_1_deg5.19
r_scbond_it2.248
r_mcangle_it2.075
r_mcbond_it1.478
r_mcbond_other1.478
r_angle_refined_deg1.235
r_angle_other_deg0.886
r_chiral_restr0.069
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.003
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
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 Atoms4650
Nucleic Acid Atoms
Solvent Atoms375
Heterogen Atoms150

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing