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Structural studies of protein tyrosine phosphatase beta catalytic domain in complex with a sulfamic acid (soaking experiment)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I4E PDB ENTRY 2I4E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.1 298 20% PEG 8000, 200 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 2.19 43.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.852 α = 90 b = 69.61 β = 90 c = 117.777 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 2005-02-02 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 1.65 34.2 73.9 0.038 15.1 2.5 29360 29360 22.77
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 1.65 1.75 39.3 0.33 3 2.1
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 2I4E 1.65 34.2 29349 29349 1467 74.05 0.178 0.17 0.176 0.1763 0.22 0.2209 RANDOM 24.874
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] 0.08 0.47 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.931 r_dihedral_angle_4_deg 14.78 r_dihedral_angle_3_deg 14.665 r_dihedral_angle_1_deg 7.273 r_scangle_it 5.225 r_scbond_it 3.549 r_mcangle_it 2.275 r_angle_refined_deg 1.583 r_mcbond_it 1.547 r_symmetry_hbond_refined 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.931 r_dihedral_angle_4_deg 14.78 r_dihedral_angle_3_deg 14.665 r_dihedral_angle_1_deg 7.273 r_scangle_it 5.225 r_scbond_it 3.549 r_mcangle_it 2.275 r_angle_refined_deg 1.583 r_mcbond_it 1.547 r_symmetry_hbond_refined 0.35 r_nbtor_refined 0.322 r_nbd_refined 0.233 r_xyhbond_nbd_refined 0.175 r_symmetry_vdw_refined 0.169 r_chiral_restr 0.126 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2362 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 38
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