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Crystal Structure of Human B-form Low Molecular Weight Phosphotyrosyl Phosphatase at 1.6 Angstrom Resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5PNT pdb entry 5pnt
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 PEGmme 5000, ammonium sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.63 24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.258 α = 90 b = 35.481 β = 99.97 c = 60.375 γ = 90
Symmetry Space Group P 1 21 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 CUSTOM-MADE 2003-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.0332 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.63 59.8 95.9 15826 15805 1 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.63 1.68 88.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 5pnt 1.63 59.76 1 15805 14246 1580 95.49 0.185 0.16371 0.15797 0.21566 0.2331 RANDOM 17.883
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] -0.27 0.33 0.5 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.281 r_scangle_it 4.332 r_scbond_it 2.812 r_mcangle_it 1.912 r_angle_refined_deg 1.762 r_mcbond_it 1.106 r_angle_other_deg 0.982 r_symmetry_vdw_other 0.302 r_nbd_other 0.254 r_nbd_refined 0.222
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.281 r_scangle_it 4.332 r_scbond_it 2.812 r_mcangle_it 1.912 r_angle_refined_deg 1.762 r_mcbond_it 1.106 r_angle_other_deg 0.982 r_symmetry_vdw_other 0.302 r_nbd_other 0.254 r_nbd_refined 0.222 r_symmetry_vdw_refined 0.183 r_symmetry_hbond_refined 0.164 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.124 r_nbtor_other 0.089 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1251 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing