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Nitrate in the active site of PTP1b is a putative mimetic of the transition state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AJ5 PDB ENTRY 3AJ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.1 281 100 MM HEPES PH 8.1, 25.4% PEG 4000, 225 MM MGNO3 AT 281K.
Crystal Properties Matthews coefficient Solvent content 2.79 55.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.62 α = 90 b = 66.765 β = 95.01 c = 68.771 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 ADSC CCD MIRRORS 2012-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 Australian Synchrotron MX1
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 2.06 80.5 99 0.05 23.6 7.1 44854
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 2.06 2.17 93.5 0.61 2.6 4.6
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3AJ5 2.06 68.6 42525 2290 98.88 0.21652 0.21529 0.23932 0.2213 RANDOM 49.386
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] -2.19 0.07 2.15 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.53 r_dihedral_angle_4_deg 17.425 r_dihedral_angle_3_deg 14.567 r_long_range_B_refined 8.156 r_long_range_B_other 8.155 r_scangle_other 6.257 r_dihedral_angle_1_deg 5.637 r_mcangle_it 5.394 r_mcangle_other 5.394 r_scbond_it 4.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.53 r_dihedral_angle_4_deg 17.425 r_dihedral_angle_3_deg 14.567 r_long_range_B_refined 8.156 r_long_range_B_other 8.155 r_scangle_other 6.257 r_dihedral_angle_1_deg 5.637 r_mcangle_it 5.394 r_mcangle_other 5.394 r_scbond_it 4.078 r_scbond_other 4.076 r_mcbond_it 3.853 r_mcbond_other 3.851 r_angle_refined_deg 1.235 r_angle_other_deg 0.901 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4671 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing