3BRB

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5290MER protein (38 mg/mL) was pre-incubated with 2.5 mM ATP and 10 mM MgCl2 for 3 hours at room temperature. Crystals were obtained at 290K against 29% PEG 400, 0.2M MgCl2, and 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.2645.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.385α = 90
b = 89.88β = 103.09
c = 69.537γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 270Rh coated Si mirrors2007-07-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE F10.91790CHESSF1

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
11.925.0598.30.0924.17.24980249802-3
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)
11.91.9788.70.6592.39295.2

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 2P0C1.925.054952547038248798.320.194690.192210.24RANDOM33.967
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]
6.060.38-2.51-3.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.761
r_dihedral_angle_4_deg20.243
r_dihedral_angle_3_deg15.047
r_dihedral_angle_1_deg5.58
r_scangle_it4.712
r_scbond_it3.602
r_mcangle_it2.686
r_mcbond_it1.904
r_angle_refined_deg1.511
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.761
r_dihedral_angle_4_deg20.243
r_dihedral_angle_3_deg15.047
r_dihedral_angle_1_deg5.58
r_scangle_it4.712
r_scbond_it3.602
r_mcangle_it2.686
r_mcbond_it1.904
r_angle_refined_deg1.511
r_nbtor_refined0.306
r_nbd_refined0.202
r_symmetry_vdw_refined0.173
r_xyhbond_nbd_refined0.137
r_symmetry_hbond_refined0.121
r_chiral_restr0.103
r_bond_refined_d0.013
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4126
Nucleic Acid Atoms
Solvent Atoms232
Heterogen Atoms67

Software

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