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Crystal structure of Phosphotyrosine-binding domain from the Human Tensin-like C1 domain-containing phosphatase (TENC1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WVH Poly-Alanine model of the PDB entry 1WVH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 294 100mM Sodium Acetate pH 4 + 2% Glycerol + 2000mM
Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.58 65.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.909 α = 90 b = 108.909 β = 90 c = 36.196 γ = 120
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 MAR CCD 165 mm 2009-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 47.14 100 0.118 8.3 10.9 23089 25.92
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 100 0.637 3 10.7 3337
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 Poly-Alanine model
of the PDB entry 1WVH 1.8 26.16 23037 1182 100 0.214 0.212 0.2267 0.242 0.2545 RANDOM 33.104
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] 0.02 0.01 0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.696 r_dihedral_angle_4_deg 15.098 r_dihedral_angle_3_deg 10.74 r_dihedral_angle_1_deg 5.917 r_scangle_it 3.216 r_scbond_it 2.126 r_mcangle_it 1.804 r_angle_refined_deg 1.382 r_mcbond_it 1.186 r_angle_other_deg 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.696 r_dihedral_angle_4_deg 15.098 r_dihedral_angle_3_deg 10.74 r_dihedral_angle_1_deg 5.917 r_scangle_it 3.216 r_scbond_it 2.126 r_mcangle_it 1.804 r_angle_refined_deg 1.382 r_mcbond_it 1.186 r_angle_other_deg 0.86 r_mcbond_other 0.244 r_symmetry_vdw_other 0.218 r_nbd_refined 0.2 r_nbd_other 0.199 r_nbtor_refined 0.175 r_symmetry_hbond_refined 0.153 r_xyhbond_nbd_refined 0.142 r_symmetry_vdw_refined 0.119 r_chiral_restr 0.087 r_nbtor_other 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1040 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling PHASER phasing