4XG8 | pdb_00004xg8

Crystal structure of an inhibitor-bound Syk


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4XG2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.527810~20%(v/v) PEG3350, 100 mM Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.1141.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.964α = 99.97
b = 42.212β = 90.5
c = 87.72γ = 101.05
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 2102011-11-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B11.0000SPring-8BL26B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.4509723.833.720930
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.44

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4XG22.435.11219912101096.030.248710.247390.250.274870.28RANDOM56.362
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]
-0.83-1.97-0.63.930.27-2.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.889
r_dihedral_angle_4_deg17.548
r_dihedral_angle_3_deg15.144
r_long_range_B_refined7.607
r_long_range_B_other7.607
r_dihedral_angle_1_deg6.688
r_scangle_other5.076
r_mcangle_it5.021
r_mcangle_other5.021
r_mcbond_it3.258
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.889
r_dihedral_angle_4_deg17.548
r_dihedral_angle_3_deg15.144
r_long_range_B_refined7.607
r_long_range_B_other7.607
r_dihedral_angle_1_deg6.688
r_scangle_other5.076
r_mcangle_it5.021
r_mcangle_other5.021
r_mcbond_it3.258
r_mcbond_other3.247
r_scbond_it3.243
r_scbond_other3.243
r_angle_refined_deg1.534
r_angle_other_deg1.065
r_chiral_restr0.083
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.004
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4146
Nucleic Acid Atoms
Solvent Atoms32
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing