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Crystal structure of PTP1B with a monocyclic thiophene inhibitor
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 15% PEG 4000, 0.1M Hepes, 0.2M MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.33 63.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.996 α = 90 b = 87.996 β = 90 c = 103.722 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 113 IMAGE PLATE RIGAKU RAXIS IV 2002-01-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.3 20 100 18915 18915 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.364 100
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.3 19.57 19876 18915 961 100 0.211 0.211 0.208 0.2155 0.26 0.2513 RANDOM 65.092
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] -1.78 -0.89 -1.78 2.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.525 r_dihedral_angle_4_deg 18.185 r_dihedral_angle_3_deg 15.04 r_dihedral_angle_1_deg 5.794 r_scangle_it 2.703 r_scbond_it 1.747 r_angle_refined_deg 1.267 r_mcangle_it 1.15 r_mcbond_it 0.695 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.525 r_dihedral_angle_4_deg 18.185 r_dihedral_angle_3_deg 15.04 r_dihedral_angle_1_deg 5.794 r_scangle_it 2.703 r_scbond_it 1.747 r_angle_refined_deg 1.267 r_mcangle_it 1.15 r_mcbond_it 0.695 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.208 r_symmetry_hbond_refined 0.204 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2427 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADSC data collection DENZO data reduction SCALEPACK data scaling CNS phasing