7GTJ

PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00000280c


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Crystal Properties
Matthews coefficientSolvent content
3.3563.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.07α = 90
b = 90.07β = 90
c = 106.894γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-09-25SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92819DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)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
11.8378.00399.90.0960.1070.99711.5285121-335.389
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.831.9499.41.0121.1330.5021.38

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.8363.0142756175399.940.19750.1960.233RANDOM32.828
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]
0.220.110.22-0.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.835
r_dihedral_angle_4_deg21.53
r_dihedral_angle_3_deg15.005
r_dihedral_angle_1_deg6.53
r_mcangle_it4.202
r_mcbond_it3.021
r_mcbond_other2.954
r_angle_refined_deg1.654
r_angle_other_deg1.406
r_chiral_restr0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.835
r_dihedral_angle_4_deg21.53
r_dihedral_angle_3_deg15.005
r_dihedral_angle_1_deg6.53
r_mcangle_it4.202
r_mcbond_it3.021
r_mcbond_other2.954
r_angle_refined_deg1.654
r_angle_other_deg1.406
r_chiral_restr0.09
r_bond_refined_d0.038
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2317
Nucleic Acid Atoms
Solvent Atoms242
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction