2YD6

Crystal structure of the N-terminal Ig1-2 module of Human Receptor Protein Tyrosine Phosphatase Delta


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.60.085M TRI-SODIUM CITRATE DIHYDRATE, 25% PEG 4000, 15% GLYCEROL, PH 5.6 .
Crystal Properties
Matthews coefficientSolvent content
2.1344

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.71α = 90
b = 48.71β = 90
c = 145.91γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

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
11.354999.90.1117.41545165-3
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)
11.351.498.80.823.110.4

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2YD41.3548.6442829225099.90.1420.1410.171RANDOM12.34
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]
-0.02-0.01-0.020.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.625
r_dihedral_angle_4_deg14.246
r_sphericity_free12.543
r_dihedral_angle_3_deg11.884
r_sphericity_bonded7.977
r_dihedral_angle_1_deg6.704
r_rigid_bond_restr4.991
r_angle_refined_deg1.646
r_angle_other_deg0.855
r_chiral_restr0.267
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.625
r_dihedral_angle_4_deg14.246
r_sphericity_free12.543
r_dihedral_angle_3_deg11.884
r_sphericity_bonded7.977
r_dihedral_angle_1_deg6.704
r_rigid_bond_restr4.991
r_angle_refined_deg1.646
r_angle_other_deg0.855
r_chiral_restr0.267
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1507
Nucleic Acid Atoms
Solvent Atoms254
Heterogen Atoms14

Software

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