2I75

Crystal Structure of Human Protein Tyrosine Phosphatase N4 (PTPN4)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2B49 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.82930.1M HEPES, 0.1 M NaCl, 1.3 M (NH4)SO4. , pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0138.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.075α = 90
b = 66.075β = 90
c = 144.508γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.979SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.4538.9295.61190111901
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.452.5898.6

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2B492.4538.92112491124958295.380.226710.223590.29104RANDOM25.129
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]
2.222.22-4.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.601
r_dihedral_angle_4_deg16.13
r_dihedral_angle_3_deg16.128
r_dihedral_angle_1_deg6.622
r_scangle_it1.693
r_angle_refined_deg1.347
r_scbond_it1.111
r_angle_other_deg1.089
r_mcangle_it0.724
r_mcbond_it0.459
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.601
r_dihedral_angle_4_deg16.13
r_dihedral_angle_3_deg16.128
r_dihedral_angle_1_deg6.622
r_scangle_it1.693
r_angle_refined_deg1.347
r_scbond_it1.111
r_angle_other_deg1.089
r_mcangle_it0.724
r_mcbond_it0.459
r_symmetry_vdw_refined0.214
r_nbd_refined0.211
r_symmetry_vdw_other0.201
r_nbd_other0.196
r_nbtor_refined0.183
r_xyhbond_nbd_refined0.158
r_chiral_restr0.131
r_symmetry_hbond_refined0.111
r_nbtor_other0.087
r_mcbond_other0.086
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2089
Nucleic Acid Atoms
Solvent Atoms51
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
PHASERphasing