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CRYSTAL STRUCTURE OF THE HUMAN PROTEIN TYROSINE PHOSPHATASE PTPN5 AT 1.8A RESOLUTION
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 SITTING DROP, 25% PEG3350, 0.2M LI2SO4, 100MM BIS TRIS PROPANE PH 5.5
Crystal Properties Matthews coefficient Solvent content 2.5 50.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.957 α = 90 b = 64.01 β = 90 c = 136.149 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 2005-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 1.8 39.96 98.7 0.06 12.9 4.9 32877 2.5
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 1.8 1.9 95.4 0.37 2.5 2.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BIJ 1.8 68.04 31160 1665 98.7 0.166 0.164 0.201 0.2279 RANDOM 17.76
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] 0.36 -0.41 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.983 r_dihedral_angle_4_deg 12.622 r_dihedral_angle_3_deg 12.096 r_dihedral_angle_1_deg 5.503 r_scangle_it 2.662 r_scbond_it 1.773 r_angle_refined_deg 1.322 r_mcangle_it 1.122 r_angle_other_deg 0.783 r_mcbond_it 0.715
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.983 r_dihedral_angle_4_deg 12.622 r_dihedral_angle_3_deg 12.096 r_dihedral_angle_1_deg 5.503 r_scangle_it 2.662 r_scbond_it 1.773 r_angle_refined_deg 1.322 r_mcangle_it 1.122 r_angle_other_deg 0.783 r_mcbond_it 0.715 r_symmetry_vdw_other 0.304 r_symmetry_vdw_refined 0.27 r_nbd_refined 0.253 r_symmetry_hbond_refined 0.191 r_xyhbond_nbd_refined 0.19 r_nbd_other 0.183 r_nbtor_refined 0.178 r_nbtor_other 0.082 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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 2239 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing