4PBW

Crystal structure of chicken receptor protein tyrosine phosphatase sigma in complex with TrkC


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7293.510% w/v PEG MME 5k, 0.1 M HEPES pH 7, 5% w/v Tacsimate
Crystal Properties
Matthews coefficientSolvent content
3.7166.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.42α = 73.37
b = 93.12β = 89.45
c = 99.38γ = 74.23
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2013-04-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
13.0581.0296.30.0698.81.851063
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.053.1396.60.3471.51.8

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 REPLACEMENTTHROUGHOUT2YD43.0594.9648530253396.230.226820.22610.23994RANDOM115.246
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]
-5.062.722.240.86-5.081.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.552
r_dihedral_angle_3_deg14.676
r_dihedral_angle_4_deg12.754
r_dihedral_angle_1_deg5.68
r_long_range_B_refined5.663
r_long_range_B_other5.663
r_scangle_other3.773
r_mcangle_it3.206
r_mcangle_other3.206
r_scbond_it2.231
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.552
r_dihedral_angle_3_deg14.676
r_dihedral_angle_4_deg12.754
r_dihedral_angle_1_deg5.68
r_long_range_B_refined5.663
r_long_range_B_other5.663
r_scangle_other3.773
r_mcangle_it3.206
r_mcangle_other3.206
r_scbond_it2.231
r_scbond_other2.23
r_mcbond_it1.913
r_mcbond_other1.913
r_angle_refined_deg1.045
r_angle_other_deg0.769
r_chiral_restr0.062
r_bond_refined_d0.006
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 Atoms10630
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing