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Structural studies of protein tyrosine phosphatase beta catalytic domain co-crystallized with a sulfamic acid inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HC1 PDB ENTRY 2HC1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.1 298 20% PEG 8000, 220 mM MgCl2, 80 mM NH4OAc, 1% BME, 0.1% BOG, 5mM DTT, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.96 37.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.313 α = 90 b = 38.795 β = 104.94 c = 66.983 γ = 90
Symmetry Space Group C 1 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 100 CCD MARRESEARCH Si monochromator 2005-03-03 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 2.15 27.37 99.5 0.063 12.48 4 15799 15799 21.36
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 97.2 0.187 5.26 4.2 2150
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 2HC1 2.15 27.37 15799 15799 791 99.55 0.173 0.17 0.169 0.169 0.246 0.2406 RANDOM 15.737
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] 1.34 0.19 -0.4 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.336 r_dihedral_angle_3_deg 17.205 r_dihedral_angle_4_deg 12.007 r_dihedral_angle_1_deg 7.925 r_scangle_it 6.16 r_scbond_it 4.273 r_mcangle_it 2.56 r_angle_refined_deg 1.843 r_mcbond_it 1.632 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.336 r_dihedral_angle_3_deg 17.205 r_dihedral_angle_4_deg 12.007 r_dihedral_angle_1_deg 7.925 r_scangle_it 6.16 r_scbond_it 4.273 r_mcangle_it 2.56 r_angle_refined_deg 1.843 r_mcbond_it 1.632 r_nbtor_refined 0.315 r_symmetry_hbond_refined 0.285 r_symmetry_vdw_refined 0.251 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.181 r_chiral_restr 0.158 r_symmetry_metal_ion_refined 0.018 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_metal_ion_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2294 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 39
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