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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 1RPM PDB ENTRY 1RPM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 298 21% PEG 8000, 220 mM MgCl2, 1% BME, 0.1% BOG, 5mM DTT, pH 8.0, vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.15 42.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.144 α = 90 b = 71.724 β = 93.41 c = 70.297 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 2006-01-01 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 2.3 30 95 0.045 15.69 2.3 32002 32002 31.1
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 2.15 2.25 68.7 0.28 3.76 1.6 2904
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 1RPM 2.3 30 27353 27353 1379 99.24 0.192 0.19 0.189 0.1884 0.244 0.2421 RANDOM 29.586
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] 1.3 -0.21 -0.55 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.432 r_dihedral_angle_4_deg 21.923 r_dihedral_angle_3_deg 19.167 r_dihedral_angle_1_deg 8.779 r_scangle_it 6.507 r_scbond_it 4.66 r_mcangle_it 3.114 r_angle_refined_deg 2.162 r_mcbond_it 2.041 r_symmetry_hbond_refined 0.772
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.432 r_dihedral_angle_4_deg 21.923 r_dihedral_angle_3_deg 19.167 r_dihedral_angle_1_deg 8.779 r_scangle_it 6.507 r_scbond_it 4.66 r_mcangle_it 3.114 r_angle_refined_deg 2.162 r_mcbond_it 2.041 r_symmetry_hbond_refined 0.772 r_symmetry_vdw_refined 0.448 r_nbtor_refined 0.327 r_nbd_refined 0.256 r_xyhbond_nbd_refined 0.186 r_chiral_restr 0.162 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4584 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection HKL-2000 data scaling AMoRE phasing