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Wildtype PTP1b in complex with DES5743
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 2.27 45.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.07 α = 90 b = 88.07 β = 90 c = 162.36 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 2017-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
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 77.53 99.8 0.083 0.026 0.999 16.2 10.8 96712
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 99.3 0.897 0.454 0.51 1.6 4.6
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 77.53 91827 4778 99.81 0.17078 0.16933 0.18 0.19844 0.206 RANDOM 24.808
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] -0.73 -0.73 1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.82 r_dihedral_angle_4_deg 18.522 r_dihedral_angle_3_deg 13.536 r_long_range_B_refined 7.577 r_long_range_B_other 7.576 r_scangle_other 6.245 r_dihedral_angle_1_deg 5.701 r_scbond_it 4.16 r_scbond_other 4.159 r_mcangle_it 3.545
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.82 r_dihedral_angle_4_deg 18.522 r_dihedral_angle_3_deg 13.536 r_long_range_B_refined 7.577 r_long_range_B_other 7.576 r_scangle_other 6.245 r_dihedral_angle_1_deg 5.701 r_scbond_it 4.16 r_scbond_other 4.159 r_mcangle_it 3.545 r_mcangle_other 3.545 r_mcbond_it 2.493 r_mcbond_other 2.493 r_angle_refined_deg 2.218 r_angle_other_deg 1.145 r_chiral_restr 0.136 r_bond_refined_d 0.024 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4770 Nucleic Acid Atoms Solvent Atoms 360 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing