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Crystal structure of human protein tyrosine phosphatase PTPN9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HNQ PDB entry 2HNQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.15 293 25% PEG 3350, 0.2 M Potassium thiocyanate, 10% Ethylene glycol, 0.1 M Bis-Tris propane pH 6.15, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.99 38.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.965 α = 77.44 b = 57.427 β = 78.22 c = 66.446 γ = 80.41
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 2007-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.95370 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 1.6 33.96 96.9 0.063 0.063 9 2 71616 71616 13.9
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 1.6 1.69 95.3 0.379 0.379 2.1 1.9 19981
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 entry 2HNQ 1.6 33.96 68013 68013 3602 96.94 0.15726 0.15726 0.15559 0.1685 0.18792 0.1982 RANDOM 11.67
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] 0.19 -0.14 0.07 0.13 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.278 r_dihedral_angle_4_deg 14.843 r_dihedral_angle_3_deg 11.354 r_scangle_it 8.173 r_scbond_it 5.985 r_dihedral_angle_1_deg 5.578 r_mcangle_it 4.264 r_mcbond_it 3.055 r_mcbond_other 1.898 r_angle_refined_deg 1.434
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.278 r_dihedral_angle_4_deg 14.843 r_dihedral_angle_3_deg 11.354 r_scangle_it 8.173 r_scbond_it 5.985 r_dihedral_angle_1_deg 5.578 r_mcangle_it 4.264 r_mcbond_it 3.055 r_mcbond_other 1.898 r_angle_refined_deg 1.434 r_angle_other_deg 1.153 r_symmetry_vdw_other 0.239 r_nbd_refined 0.225 r_nbd_other 0.2 r_nbtor_refined 0.184 r_symmetry_vdw_refined 0.169 r_symmetry_hbond_refined 0.158 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.09 r_nbtor_other 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4637 Nucleic Acid Atoms Solvent Atoms 405 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction CCP4 data scaling PHASER phasing