3SRV

Crystal structure of spleen tyrosine kinase (SYK) in complex with a diaminopyrimidine carboxamide inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherOTHER IN-HOUSE COORDINATES

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529320% PEG3350, 0.2M Na-K-Phosphate, 0.1M Bis-Tris-Propane pH 6.5, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2545.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.124α = 99.68
b = 42.316β = 90.16
c = 87.621γ = 100.19
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.9763ESRFID29

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
11.9539.4794.70.05211.11.9385893858925.7
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)
11.952.0694.70.4020.4021.71.95634

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 SYNTHESISTHROUGHOUTOTHER IN-HOUSE COORDINATES1.95203856619291000.18750.18460.241RANDOM35.6065
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]
-0.71-1.130.191.610.69-1.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.25
r_dihedral_angle_4_deg16.99
r_dihedral_angle_3_deg13.965
r_dihedral_angle_1_deg4.399
r_scangle_it4.399
r_scbond_it2.875
r_mcangle_it2.187
r_angle_refined_deg1.378
r_mcbond_it1.218
r_angle_other_deg0.881
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.25
r_dihedral_angle_4_deg16.99
r_dihedral_angle_3_deg13.965
r_dihedral_angle_1_deg4.399
r_scangle_it4.399
r_scbond_it2.875
r_mcangle_it2.187
r_angle_refined_deg1.378
r_mcbond_it1.218
r_angle_other_deg0.881
r_mcbond_other0.245
r_chiral_restr0.088
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4292
Nucleic Acid Atoms
Solvent Atoms472
Heterogen Atoms74

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
REFMACphasing