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Crystal Structure of Human Protein Tyrosine Phosphatase N4 (PTPN4)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B49
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.8 293 0.1M HEPES, 0.1 M NaCl, 1.3 M (NH4)SO4. , pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.01 38.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.075 α = 90 b = 66.075 β = 90 c = 144.508 γ = 90
Symmetry Space Group P 41 21 2
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 2006-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.979 SLS X10SA
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 2.45 38.92 95.6 11901 11901
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 2.45 2.58 98.6
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 (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 2B49 2.45 38.92 11249 11249 582 95.38 0.22671 0.22359 0.2251 0.29104 0.2928 RANDOM 25.129
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] 2.22 2.22 -4.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.601 r_dihedral_angle_4_deg 16.13 r_dihedral_angle_3_deg 16.128 r_dihedral_angle_1_deg 6.622 r_scangle_it 1.693 r_angle_refined_deg 1.347 r_scbond_it 1.111 r_angle_other_deg 1.089 r_mcangle_it 0.724 r_mcbond_it 0.459
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.601 r_dihedral_angle_4_deg 16.13 r_dihedral_angle_3_deg 16.128 r_dihedral_angle_1_deg 6.622 r_scangle_it 1.693 r_angle_refined_deg 1.347 r_scbond_it 1.111 r_angle_other_deg 1.089 r_mcangle_it 0.724 r_mcbond_it 0.459 r_symmetry_vdw_refined 0.214 r_nbd_refined 0.211 r_symmetry_vdw_other 0.201 r_nbd_other 0.196 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.131 r_symmetry_hbond_refined 0.111 r_nbtor_other 0.087 r_mcbond_other 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2089 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling PHASER phasing