4UXL

Structure of Human ROS1 Kinase Domain in Complex with PF-06463922


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZBFPDB ENTRY 3ZBF

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 PF-06463922 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
2.755

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.844α = 90
b = 105.844β = 90
c = 49.843γ = 120
Symmetry
Space GroupP 64

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray87PIXELDECTRIS PILATUS 6M2012-04-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-IDAPS17-ID

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
12.2191.6697.10.04276.715684241.4
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)
12.212.3362.10.422.84.4

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 3ZBF2.491.66126483791000.2110.2110.281RANDOM50.4
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]
-5.982.43-5.9811.97
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.8
c_scangle_it3.11
c_mcangle_it2.82
c_scbond_it2.13
c_mcbond_it1.66
c_angle_deg0.9
c_improper_angle_d0.62
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.8
c_scangle_it3.11
c_mcangle_it2.82
c_scbond_it2.13
c_mcbond_it1.66
c_angle_deg0.9
c_improper_angle_d0.62
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 Atoms2310
Nucleic Acid Atoms
Solvent Atoms136
Heterogen Atoms30

Software

Software
Software NamePurpose
CNSrefinement
autoPROCdata reduction
SCALAdata scaling
CNXphasing