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Crystal Structure of the Catalytic Domain of Human Protein Tyrosine Phosphatase non-receptor Type 18
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B49 pdb entries 2B49, 1GWZ experimental model PDB 1GWZ pdb entries 2B49, 1GWZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.8 277 0.1M HEPES, 25% PEG-3350, 6% Jeffamine M-600, pH 6.8, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.06 40.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.338 α = 90 b = 63.763 β = 102.64 c = 48.992 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 MARMOSAIC 225 mm CCD 2006-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.5 38.24 99.3 0.065 0.065 12.4 3.7 44277 13.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.5 1.58 95.2 0.343 0.343 3.4 3.1 19366
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 entries 2B49, 1GWZ 1.5 38.24 42028 42028 2228 99.25 0.15557 0.15557 0.15407 0.162 0.18395 0.1858 RANDOM 11.822
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] -0.11 0.24 -0.3 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.923 r_dihedral_angle_4_deg 17.219 r_dihedral_angle_3_deg 11.71 r_scangle_it 6.543 r_dihedral_angle_1_deg 5.659 r_scbond_it 5.071 r_mcangle_it 4.052 r_mcbond_it 3.364 r_angle_refined_deg 1.471 r_mcbond_other 1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.923 r_dihedral_angle_4_deg 17.219 r_dihedral_angle_3_deg 11.71 r_scangle_it 6.543 r_dihedral_angle_1_deg 5.659 r_scbond_it 5.071 r_mcangle_it 4.052 r_mcbond_it 3.364 r_angle_refined_deg 1.471 r_mcbond_other 1.08 r_angle_other_deg 0.93 r_symmetry_vdw_other 0.293 r_nbd_refined 0.216 r_nbd_other 0.204 r_nbtor_refined 0.181 r_symmetry_hbond_refined 0.179 r_xyhbond_nbd_refined 0.145 r_symmetry_vdw_refined 0.127 r_chiral_restr 0.09 r_nbtor_other 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2228 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction CCP4 data scaling PHASER phasing