2YD4

Crystal structure of the N-terminal Ig1-2 module of Chicken Receptor Protein Tyrosine Phosphatase Sigma


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
19.620% W/V PEG 8000, 0.1M CHES, PH 9.6 .
Crystal Properties
Matthews coefficientSolvent content
2.857

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.745α = 90
b = 104.745β = 90
c = 94.61γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
11.65741000.1226.22631882-317.51
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)
11.651.71000.884.218.6

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 DIFFRACTIONSADTHROUGHOUTNONE1.6574.0730242162399.970.180790.179640.20229RANDOM18.706
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]
-0.14-0.140.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.743
r_dihedral_angle_4_deg14.827
r_dihedral_angle_3_deg12.531
r_dihedral_angle_1_deg6.492
r_angle_refined_deg1.421
r_angle_other_deg0.832
r_chiral_restr0.086
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.743
r_dihedral_angle_4_deg14.827
r_dihedral_angle_3_deg12.531
r_dihedral_angle_1_deg6.492
r_angle_refined_deg1.421
r_angle_other_deg0.832
r_chiral_restr0.086
r_bond_refined_d0.012
r_gen_planes_refined0.006
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1567
Nucleic Acid Atoms
Solvent Atoms279
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
XDSdata reduction
xia2data scaling
SCALAdata scaling
SHELXDphasing