4XG2

Crystal structure of ligand-free Syk


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.527810~20%(v/v) PEG3350, 100 mM Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.0640.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.189α = 90
b = 84.799β = 98.74
c = 41.406γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-05-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 5C (4A)1.0000PAL/PLS5C (4A)

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
12.25099.140.797.413725
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.24

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 REPLACEMENTTHROUGHOUT1XBA2.2142.41304167898.890.204270.203120.22681RANDOM43.142
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]
-2.13-2.2-1.33.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.122
r_dihedral_angle_4_deg16.768
r_dihedral_angle_3_deg13.026
r_dihedral_angle_1_deg6.025
r_long_range_B_refined4.747
r_long_range_B_other4.715
r_mcangle_it2.892
r_mcangle_other2.891
r_scangle_other2.878
r_mcbond_it1.716
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.122
r_dihedral_angle_4_deg16.768
r_dihedral_angle_3_deg13.026
r_dihedral_angle_1_deg6.025
r_long_range_B_refined4.747
r_long_range_B_other4.715
r_mcangle_it2.892
r_mcangle_other2.891
r_scangle_other2.878
r_mcbond_it1.716
r_mcbond_other1.714
r_scbond_it1.701
r_scbond_other1.701
r_angle_refined_deg1.124
r_angle_other_deg0.924
r_chiral_restr0.069
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.002
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 Atoms2117
Nucleic Acid Atoms
Solvent Atoms82
Heterogen Atoms

Software

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