6HM6

CRYSTAL STRUCTURE OF SPLEEN TYROSINE KINASE (SYK) IN COMPLEX WITH A 2-(PYRIDINYLOXYMETHYL)PYRIDINE INHIBITOR


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherOther in-house coordinates

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293PEG 1500, HEPES, glycerol, tacsimate.
Crystal Properties
Matthews coefficientSolvent content
2.0740.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.437α = 90
b = 84.982β = 100.5
c = 40.277γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN A2002009-07-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.142.4998.90.0520.0619.93.531512450.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1899.90.4370.51723.47

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 coordinates2.1201433476298.760.21670.21280.2903RANDOM65.046
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]
6.92-0.65-3.19-3.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.518
r_dihedral_angle_4_deg18.837
r_dihedral_angle_3_deg12.049
r_dihedral_angle_1_deg4.014
r_angle_refined_deg1.264
r_angle_other_deg0.881
r_chiral_restr0.078
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.518
r_dihedral_angle_4_deg18.837
r_dihedral_angle_3_deg12.049
r_dihedral_angle_1_deg4.014
r_angle_refined_deg1.264
r_angle_other_deg0.881
r_chiral_restr0.078
r_bond_refined_d0.008
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 Atoms2121
Nucleic Acid Atoms
Solvent Atoms119
Heterogen Atoms27

Software

Software
Software NamePurpose
d*TREKdata reduction
d*TREKdata scaling
PDB_EXTRACTdata extraction
REFMACphasing
REFMACrefinement
Cootmodel building