☰ Navigation Tabs
Wildtype PTP1b in complex with DES4799
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other in-house structure of same protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.2 278 Reservoir solution: 50 mM MES (pH 6.2), 14% PEG6000, 50 mM MgCl2;
Protein solution: 10.3 mg/ml PTP-1B 1-298 in 25 mM Hepes pH 7.2, 150 mM NaCl, 1 mM EDTA, 2 mM DTT
Crystal Properties Matthews coefficient Solvent content 2.39 48.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.44 α = 90 b = 89.44 β = 90 c = 165.76 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2016-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.45 82.88 99.8 0.086 0.027 0.999 15.8 11.4 119149 14.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.49 99.8 1.706 0.703 0.527 1.2 7.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT in-house structure of same protein 1.45 63.32 113016 6003 99.78 0.13709 0.13438 0.1425 0.18836 0.1948 RANDOM 24.011
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] 0.88 0.88 -1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.922 r_sphericity_free 29.27 r_dihedral_angle_4_deg 20.331 r_sphericity_bonded 19.291 r_dihedral_angle_3_deg 14.229 r_scangle_other 6.269 r_long_range_B_refined 6.191 r_long_range_B_other 6.19 r_dihedral_angle_1_deg 5.948 r_rigid_bond_restr 5.364
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.922 r_sphericity_free 29.27 r_dihedral_angle_4_deg 20.331 r_sphericity_bonded 19.291 r_dihedral_angle_3_deg 14.229 r_scangle_other 6.269 r_long_range_B_refined 6.191 r_long_range_B_other 6.19 r_dihedral_angle_1_deg 5.948 r_rigid_bond_restr 5.364 r_scbond_it 5.333 r_scbond_other 5.332 r_mcangle_it 4.056 r_mcangle_other 4.055 r_mcbond_it 3.416 r_mcbond_other 3.416 r_angle_refined_deg 2.375 r_angle_other_deg 1.264 r_chiral_restr 0.157 r_bond_refined_d 0.03 r_gen_planes_refined 0.013 r_gen_planes_other 0.005 r_bond_other_d 0.002 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4751 Nucleic Acid Atoms Solvent Atoms 642 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing