3AD6

Crystal structure of Pyrazolo pyrimidine derivative bound to the kinase domain of human LCK, (auto-phosphorylated on TYR394)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LCKPDB ENTRY 3LCK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52770.2M (NH4)2SO4, 0.1M SODIUM CACODYLATE, 30% PEG 8000, 0.2% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1743.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.271α = 90
b = 73.604β = 90
c = 92.344γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDRIGAKU JUPITER 2102002-10-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL32B21.5418SPring-8BL32B2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.1528.71980.130.1557.3158751590715.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.152.2797.50.2510.2964.93.22261

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 3LCK2.151014119158897.630.191920.183160.26951RANDOM5.903
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]
0.080.79-0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.654
r_dihedral_angle_4_deg15.67
r_dihedral_angle_3_deg14.37
r_dihedral_angle_1_deg6.065
r_scangle_it3.761
r_scbond_it2.326
r_angle_refined_deg1.464
r_mcangle_it1.303
r_mcbond_it0.681
r_chiral_restr0.105
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.654
r_dihedral_angle_4_deg15.67
r_dihedral_angle_3_deg14.37
r_dihedral_angle_1_deg6.065
r_scangle_it3.761
r_scbond_it2.326
r_angle_refined_deg1.464
r_mcangle_it1.303
r_mcbond_it0.681
r_chiral_restr0.105
r_bond_refined_d0.014
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2218
Nucleic Acid Atoms
Solvent Atoms221
Heterogen Atoms41

Software

Software
Software NamePurpose
BSSdata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling