4YJP

THE KINASE DOMAIN OF HUMAN SPLEEN TYROSINE (SYK) IN COMPLEX WITH GTC000223


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherIn-house SYK model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.829330% Jeffamine ED-2001, 10% Glycerol, 0.1M MES pH6.8, 5mM TCEP
Crystal Properties
Matthews coefficientSolvent content
1.9838.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.912α = 90
b = 84.912β = 100.14
c = 39.845γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2005-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.97935ESRFID23-1

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
11.8328.8199.80.0540.05415.53.822453
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)
11.831.931000.4770.4771.53.73254

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTIn-house SYK model1.832021281114799.720.19560.19220.2576RANDOM39.304
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]
3.41-0.32-1.24-2.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.65
r_dihedral_angle_4_deg22.845
r_dihedral_angle_3_deg12.445
r_dihedral_angle_1_deg4.311
r_angle_refined_deg1.419
r_angle_other_deg0.873
r_chiral_restr0.086
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.65
r_dihedral_angle_4_deg22.845
r_dihedral_angle_3_deg12.445
r_dihedral_angle_1_deg4.311
r_angle_refined_deg1.419
r_angle_other_deg0.873
r_chiral_restr0.086
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2142
Nucleic Acid Atoms
Solvent Atoms197
Heterogen Atoms35

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction