3ZM2

Catalytic domain of human SHP2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
116-22% (W/V) PEG3350 0.1-0.2 M SODIUM CITRATE
Crystal Properties
Matthews coefficientSolvent content
2.2946.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.123α = 72.04
b = 42.061β = 80.39
c = 49.287γ = 74.65
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2009-02-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

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
11.520830.0317.72.239334
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5949.44.24

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3B7O1.519.2639064205687.290.187330.185490.22286RANDOM18.736
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]
0.08-0.030.03-0.040.11-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.14
r_dihedral_angle_4_deg21.766
r_dihedral_angle_3_deg15.636
r_dihedral_angle_1_deg6.538
r_scangle_it5.82
r_scbond_it4.14
r_mcangle_it2.716
r_angle_refined_deg2.161
r_mcbond_it1.715
r_chiral_restr0.158
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.14
r_dihedral_angle_4_deg21.766
r_dihedral_angle_3_deg15.636
r_dihedral_angle_1_deg6.538
r_scangle_it5.82
r_scbond_it4.14
r_mcangle_it2.716
r_angle_refined_deg2.161
r_mcbond_it1.715
r_chiral_restr0.158
r_bond_refined_d0.026
r_gen_planes_refined0.013
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_other
r_mcangle_other
r_scbond_other
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 Atoms2149
Nucleic Acid Atoms
Solvent Atoms205
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing