3ZBF

Structure of Human ROS1 Kinase Domain in Complex with Crizotinib


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6286CRYSTALS WERE OBTAINED BY THE HANGING DROP VAPOR DIFFUSION METHOD AT 13 DEGREES C BY MIXING 1.5 MICROLITERS OF SOLUTION CONTAINING A 1:3 MOLAR RATIO OF PHOSPHORYLATED ROS1 KD (12.2MG/ML) TO CRIZOTINIB AND 1.5 MICROLITERS OF RESERVOIR SOLUTION CONTAINING 25% (W/V) PEG 3350, 0.6M POTASSIUM THIOCYANATE AND 0.1M SODIUM CITRATE TRIBASIC DIHYDRATE, PH5.6. CRYSTALS WERE FLASH-FROZEN IN LIQUID NITROGEN AFTER TRANSFER TO 2 MICROLITERS OF RESERVOIR SOLUTION CONTAINING 25% (V/V) GLYCEROL AS A CRYOPROTECTANT.
Crystal Properties
Matthews coefficientSolvent content
2.7455.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.854α = 90
b = 106.854β = 90
c = 50.357γ = 120
Symmetry
Space GroupP 64

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray87CCDMARRESEARCH2012-05-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-1CLSI08ID-1

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
12.12501000.06317.881879633.9
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)
12.122.21000.593.77.4

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2XP22.244.23168631648679697.70.2360.2330.282RANDOM52.5
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]
-1.632.53-1.633.26
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.2
c_scangle_it3.22
c_mcangle_it2.66
c_scbond_it2.24
c_mcbond_it1.63
c_angle_deg0.9
c_improper_angle_d0.67
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.2
c_scangle_it3.22
c_mcangle_it2.66
c_scbond_it2.24
c_mcbond_it1.63
c_angle_deg0.9
c_improper_angle_d0.67
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2260
Nucleic Acid Atoms
Solvent Atoms137
Heterogen Atoms30

Software

Software
Software NamePurpose
CNXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNXphasing