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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 2I3R PDB ENTRY 2I3R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 278 21% PEG 8000, 220 mM MgCl2, 1% BME, 0.1% BOG, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 2.21 44.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.785 α = 90 b = 69.777 β = 90 c = 118.523 γ = 90
Symmetry Space Group P 21 21 21
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 2004-01-01 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 1.85 22.31 98.2 0.028 21.75 4.5 27971 27971 26.4
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 1.85 1.95 93.3 0.19 5.11 3.5 3939
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2I3R 1.85 22.31 27925 27925 1409 98.34 0.187 0.187 0.226 0.2358 RANDOM 30.832
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] 0.66 0.79 -1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.601 r_dihedral_angle_3_deg 15.703 r_dihedral_angle_4_deg 13.716 r_dihedral_angle_1_deg 8.983 r_scangle_it 6.81 r_scbond_it 4.783 r_mcangle_it 3.225 r_mcbond_it 2.387 r_angle_refined_deg 1.194 r_symmetry_vdw_refined 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.601 r_dihedral_angle_3_deg 15.703 r_dihedral_angle_4_deg 13.716 r_dihedral_angle_1_deg 8.983 r_scangle_it 6.81 r_scbond_it 4.783 r_mcangle_it 3.225 r_mcbond_it 2.387 r_angle_refined_deg 1.194 r_symmetry_vdw_refined 0.56 r_nbtor_refined 0.323 r_nbd_refined 0.254 r_symmetry_hbond_refined 0.242 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.106 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2264 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms
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