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Crystal structure of human tyrosine phosphatase PTPN22
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OC3 PDB entry 2OC3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.9 293 100 mM Bicine pH 7.9, 25% PEG 10000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.36 47.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.961 α = 90 b = 48.442 β = 102.84 c = 119.805 γ = 90
Symmetry Space Group P 1 21 1
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 0.97900 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 1.9 59.44 100 0.08 0.08 13.1 3.7 54178 54178 24.7
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 1.9 2 100 0.389 0.389 3.3 3.6
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 (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 2OC3 1.9 59.44 51408 51408 2761 99.96 0.16627 0.16627 0.16352 0.1729 0.21725 0.2267 RANDOM 30.663
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] -0.14 0.41 0.5 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.784 r_dihedral_angle_4_deg 14.162 r_dihedral_angle_3_deg 14.027 r_scangle_it 9.561 r_scbond_it 8.346 r_dihedral_angle_1_deg 6.145 r_mcangle_it 5.956 r_mcbond_it 5.098 r_mcbond_other 2.414 r_angle_refined_deg 1.518
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.784 r_dihedral_angle_4_deg 14.162 r_dihedral_angle_3_deg 14.027 r_scangle_it 9.561 r_scbond_it 8.346 r_dihedral_angle_1_deg 6.145 r_mcangle_it 5.956 r_mcbond_it 5.098 r_mcbond_other 2.414 r_angle_refined_deg 1.518 r_angle_other_deg 0.941 r_symmetry_vdw_other 0.284 r_nbd_refined 0.213 r_nbd_other 0.206 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.169 r_symmetry_hbond_refined 0.142 r_chiral_restr 0.094 r_nbtor_other 0.087 r_symmetry_vdw_refined 0.079 r_xyhbond_nbd_other 0.024 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4830 Nucleic Acid Atoms Solvent Atoms 369 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction CCP4 data scaling PHASER phasing