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CRYSTAL STRUCTURE OF THE MOUSE PROTEIN TYROSINE PHOSPHATASE PTPN5 (STEP) IN COMPLEX WITH COMPOUND BI-0314
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BIJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 277 26% PEG 3350, 0.1 M Tris pH 7.8, 0.2 M ammonium citrate
Crystal Properties Matthews coefficient Solvent content 2.36 47.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.303 α = 90 b = 59.303 β = 90 c = 181.641 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 PIXEL DECTRIS PILATUS 2M-F 2016-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00000 SLS X06DA
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 1.771 56.3745 78.6 0.212 0.212 11.4 12.7 25620 21.69
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 1.771 1.927 18 1.793 1.793 1.5 10.9
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 2BIJ 1.771 28.19 25606 1255 78.7 0.183 0.181 0.1867 0.212 0.217 RANDOM 27.88
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] 0.5367 0.5367 -1.0734
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.19 t_omega_torsion 2.95 t_angle_deg 0.96 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.19 t_omega_torsion 2.95 t_angle_deg 0.96 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2373 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms 20
Software Software Software Name Purpose autoPROC data scaling Aimless data scaling BUSTER refinement Coot model building