☰ Navigation Tabs
Wildtype PTP1b in complex with DES4884
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 2.38 48.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.57 α = 90 b = 89.57 β = 90 c = 164.31 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 1.53 43.21 99.6 0.079 0.024 0.999 16.7 12 100903
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 1.53 1.57 99.9 1.945 0.694 0.55 1.1 8.8
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 1.53 43.21 95742 5035 99.58 0.15793 0.1544 0.1611 0.22259 0.2225 RANDOM 33.014
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] 1.29 1.29 -2.58
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 62.009 r_dihedral_angle_2_deg 35.291 r_sphericity_bonded 28.448 r_dihedral_angle_4_deg 17.447 r_dihedral_angle_3_deg 13.729 r_long_range_B_refined 10.523 r_long_range_B_other 10.522 r_scangle_other 9.97 r_scbond_it 8.782 r_scbond_other 8.782
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 62.009 r_dihedral_angle_2_deg 35.291 r_sphericity_bonded 28.448 r_dihedral_angle_4_deg 17.447 r_dihedral_angle_3_deg 13.729 r_long_range_B_refined 10.523 r_long_range_B_other 10.522 r_scangle_other 9.97 r_scbond_it 8.782 r_scbond_other 8.782 r_mcangle_it 6.869 r_mcangle_other 6.869 r_dihedral_angle_1_deg 6.251 r_mcbond_it 5.639 r_mcbond_other 5.638 r_rigid_bond_restr 5.521 r_angle_refined_deg 1.855 r_angle_other_deg 1.033 r_chiral_restr 0.125 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 4632 Nucleic Acid Atoms Solvent Atoms 540 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing