3ACK

Crystal structure of Pyrrolo pyrazine 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
2.1743.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.224α = 90
b = 73.714β = 90
c = 92.22γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDRIGAKU JUPITER 2102002-08-31MSINGLE 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
12.628.6999.60.0540.06519.23.49290932526.3
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)
2.62.741000.1040.12312.23.51341

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 3LCK2.610819391499.760.18030.170740.26535RANDOM26.464
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]
-0.360.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.871
r_dihedral_angle_4_deg16.967
r_dihedral_angle_3_deg14.22
r_dihedral_angle_1_deg5.651
r_scangle_it4.122
r_scbond_it2.559
r_mcangle_it1.59
r_angle_refined_deg0.92
r_mcbond_it0.832
r_chiral_restr0.066
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.871
r_dihedral_angle_4_deg16.967
r_dihedral_angle_3_deg14.22
r_dihedral_angle_1_deg5.651
r_scangle_it4.122
r_scbond_it2.559
r_mcangle_it1.59
r_angle_refined_deg0.92
r_mcbond_it0.832
r_chiral_restr0.066
r_gen_planes_refined0.013
r_bond_refined_d0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2210
Nucleic Acid Atoms
Solvent Atoms106
Heterogen Atoms35

Software

Software
Software NamePurpose
BSSdata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling