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Oxidation state of protein tyrosine phosphatase 1B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C83 PDB ENTRY 1C83
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 12-18% PEG4000, 0.1M HEPES PH 7.5, 0.2M MAGNESIUM ACETATE, 10MM DTT
Crystal Properties Matthews coefficient Solvent content 3.1 59.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.914 α = 90 b = 88.914 β = 90 c = 104.645 γ = 120
Symmetry Space Group P 31 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 RIGAKU CCD CONFOCAL MULTILAYER OPTICS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
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 2.5 76 95.9 0.172 4.6 1.8 16237
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 2.5 2.59 99.3 0.37 1.9 1.85
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1C83 2.5 76.7 15415 820 95.9 0.2 0.196 0.27 RANDOM 22.84
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] 0.34 0.17 0.34 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.479 r_scangle_it 5.875 r_mcangle_it 4.666 r_scbond_it 3.917 r_mcbond_it 3.117 r_angle_refined_deg 1.666 r_angle_other_deg 0.857 r_symmetry_hbond_refined 0.285 r_symmetry_vdw_refined 0.256 r_symmetry_vdw_other 0.255
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.479 r_scangle_it 5.875 r_mcangle_it 4.666 r_scbond_it 3.917 r_mcbond_it 3.117 r_angle_refined_deg 1.666 r_angle_other_deg 0.857 r_symmetry_hbond_refined 0.285 r_symmetry_vdw_refined 0.256 r_symmetry_vdw_other 0.255 r_nbd_other 0.246 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.2 r_nbtor_other 0.093 r_chiral_restr 0.086 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2291 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling AMoRE phasing