2NLK

Crystal structure of D1 and D2 catalytic domains of human Protein Tyrosine Phosphatase Gamma (D1+D2 PTPRG)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP827710% PEG 10K, 100mM Imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthew coefficientSolvent content
3.2762.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.51α = 90
b = 133.996β = 90
c = 59.084γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS2006-09-19MSINGLE WAVELENGTH
21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.439.93699.50.0990.0995.94.23760637418
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.5398.60.4850.4851.53.65313

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRies 2H4V, 2C7S, 1RPM, 1YF0, 1H02, 1GWZ2.439.9363763937345186499.220.2390.2390.2370.274RANDOM22.159
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]
1.32-0.78-0.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.546
r_dihedral_angle_4_deg20.899
r_dihedral_angle_3_deg14.692
r_dihedral_angle_1_deg7.626
r_scangle_it2.469
r_scbond_it1.651
r_angle_refined_deg1.565
r_mcangle_it1.066
r_angle_other_deg1.06
r_mcbond_it0.641
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.546
r_dihedral_angle_4_deg20.899
r_dihedral_angle_3_deg14.692
r_dihedral_angle_1_deg7.626
r_scangle_it2.469
r_scbond_it1.651
r_angle_refined_deg1.565
r_mcangle_it1.066
r_angle_other_deg1.06
r_mcbond_it0.641
r_symmetry_vdw_other0.196
r_nbd_refined0.195
r_nbd_other0.193
r_nbtor_refined0.176
r_xyhbond_nbd_refined0.16
r_chiral_restr0.133
r_mcbond_other0.132
r_symmetry_vdw_refined0.123
r_symmetry_hbond_refined0.103
r_nbtor_other0.087
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_gen_planes_other0.001
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4386
Nucleic Acid Atoms
Solvent Atoms150
Heterogen Atoms

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
MOSFLMdata reduction
CCP4data scaling