3ZM0

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
2.3246.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.216α = 72.52
b = 42.257β = 81.63
c = 49.197γ = 74.73
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
11.520860.0517.43.240770
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)
11.51.5951.60.025.5

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 3B7O1.519.640031210785.80.185590.184130.21342RANDOM20.499
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]
0.27-0.190.010.340.33-0.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.885
r_dihedral_angle_4_deg20.591
r_dihedral_angle_3_deg14.112
r_dihedral_angle_1_deg6.512
r_scangle_it5.37
r_scbond_it3.723
r_mcangle_it2.344
r_angle_refined_deg1.862
r_mcbond_it1.524
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.885
r_dihedral_angle_4_deg20.591
r_dihedral_angle_3_deg14.112
r_dihedral_angle_1_deg6.512
r_scangle_it5.37
r_scbond_it3.723
r_mcangle_it2.344
r_angle_refined_deg1.862
r_mcbond_it1.524
r_nbtor_refined0.311
r_nbd_refined0.239
r_symmetry_vdw_refined0.195
r_chiral_restr0.13
r_xyhbond_nbd_refined0.128
r_symmetry_hbond_refined0.116
r_bond_refined_d0.022
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms2139
Nucleic Acid Atoms
Solvent Atoms206
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing