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Structural studies of protein tyrosine phosphatase beta catalytic domain in complex with inhibitors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I3U PDB ENTRY 2I3U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 21% PEG 8000, 220 mM MgCl2, 1% BME, 0.1% BOG, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.14 42.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.058 α = 90 b = 71.721 β = 93.31 c = 69.859 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH Si monochromator 2004-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.75 38.14 97.1 0.025 24.8 3.2 59776 59776 26.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.85 97.7 0.135 7.1 2.5 8987
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 2I3U 1.75 38.1 59756 59756 3035 97.12 0.185 0.18 0.183 0.1814 0.221 0.2189 RANDOM 29.95
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] 0.02 0.52 -1.2 1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.2 r_dihedral_angle_4_deg 17.168 r_dihedral_angle_3_deg 15.364 r_dihedral_angle_1_deg 6.897 r_scangle_it 5.941 r_scbond_it 4.018 r_mcangle_it 2.824 r_mcbond_it 1.856 r_angle_refined_deg 1.673 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.2 r_dihedral_angle_4_deg 17.168 r_dihedral_angle_3_deg 15.364 r_dihedral_angle_1_deg 6.897 r_scangle_it 5.941 r_scbond_it 4.018 r_mcangle_it 2.824 r_mcbond_it 1.856 r_angle_refined_deg 1.673 r_nbtor_refined 0.317 r_symmetry_vdw_refined 0.24 r_nbd_refined 0.231 r_xyhbond_nbd_refined 0.17 r_symmetry_hbond_refined 0.148 r_chiral_restr 0.142 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4583 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing