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crystal structure of the c472s mutant of human protein tyrosine phosphatase ptpn5 (step, striatum enriched phosphatase) in complex with phosphotyrosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BIJ PDB ENTRY 2BIJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 150 NL SITTING DROPS, 0.1 M CACL2, 0.1 M TRIS PH 8, 20% PEG 6K, 10% ETHYLENE GLYCOL
Crystal Properties Matthews coefficient Solvent content 2.4 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.342 α = 90 b = 64.348 β = 90 c = 100.781 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 MIRRORS 2006-03-24 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) 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 1.7 50.39 98.5 0.07 11.92 3.4 37692 3
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 1.7 1.8 91.6 0.27 3.07 2.31
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BIJ 1.7 101.02 35803 1888 98.5 0.177 0.175 0.183 0.205 0.2128 RANDOM 12.38
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] 0.68 -0.26 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.769 r_dihedral_angle_4_deg 15.849 r_dihedral_angle_3_deg 10.922 r_scangle_it 6.32 r_dihedral_angle_1_deg 5.273 r_scbond_it 4.667 r_mcangle_it 3.653 r_mcbond_it 2.754 r_angle_refined_deg 1.107 r_angle_other_deg 0.825
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.769 r_dihedral_angle_4_deg 15.849 r_dihedral_angle_3_deg 10.922 r_scangle_it 6.32 r_dihedral_angle_1_deg 5.273 r_scbond_it 4.667 r_mcangle_it 3.653 r_mcbond_it 2.754 r_angle_refined_deg 1.107 r_angle_other_deg 0.825 r_xyhbond_nbd_refined 0.289 r_symmetry_vdw_other 0.219 r_nbd_refined 0.207 r_nbd_other 0.188 r_nbtor_refined 0.176 r_symmetry_hbond_refined 0.166 r_nbtor_other 0.081 r_symmetry_vdw_refined 0.069 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2194 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing