3BPR

Crystal structure of catalytic domain of the proto-oncogene tyrosine-protein kinase MER in complex with inhibitor C52


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2P0CPDB ENTRY 2P0C

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5287Compound C52 (50 mM in DMSO) was added to 8 mg/ml MER protein to the final concentration of 2.5 mM. The mixture was rocked at 277 K overnight and further concentrated to about 35 mg/ml. Crystals were grown by mixing 2 microliters of MER inhibitor solution and 2 microliters of reservoir solution (100 mM Tris-HCl pH 8.5, 3.64 M NaCl) at 287 K using the hanging-drop vapor-diffusion method. Crystals were cryo-protected with a solution composed of glycerol, ethylene glycol, glucose, and fructose., VAPOR DIFFUSION, HANGING DROP, pH 8.50
Crystal Properties
Matthews coefficientSolvent content
2.6954.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.001α = 90
b = 91.702β = 94.06
c = 120.745γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210MIRRORS2007-03-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-IDAPS17-ID

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
12.850990.159.13.337537-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.82.9940.532.32.9

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 2P0C2.847.33533835338188998.730.2750.273610.30134RANDOM42.487
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]
-4.241.07-4.739.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.029
r_dihedral_angle_3_deg18.727
r_dihedral_angle_4_deg17.442
r_dihedral_angle_1_deg5.649
r_scangle_it1.787
r_scbond_it1.261
r_angle_refined_deg1.239
r_mcangle_it0.794
r_mcbond_it0.49
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.029
r_dihedral_angle_3_deg18.727
r_dihedral_angle_4_deg17.442
r_dihedral_angle_1_deg5.649
r_scangle_it1.787
r_scbond_it1.261
r_angle_refined_deg1.239
r_mcangle_it0.794
r_mcbond_it0.49
r_nbtor_refined0.305
r_nbd_refined0.219
r_xyhbond_nbd_refined0.144
r_symmetry_vdw_refined0.139
r_symmetry_hbond_refined0.131
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8073
Nucleic Acid Atoms
Solvent Atoms131
Heterogen Atoms99

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing