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Structure of PTP1b complexed with difluoromethylphosphonate inhibitor Compound 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other internal model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 13-17% PEG8000, 0.3 M magnesium acetate, 0.1 M HEPES, pH 7.5-7.6
Crystal Properties Matthews coefficient Solvent content 3 63.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.254 α = 90 b = 88.254 β = 90 c = 103.843 γ = 120
Symmetry Space Group P 31 2 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 PIXEL DECTRIS EIGER X 9M 2020-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.000 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.724 76.43 99.9 0.998 14.4 9.2 45000 29.52
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.724 1.806 0.67
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.73 25.24 44576 2199 90.5 0.1856 0.1847 0.1777 0.2029 0.1967 RANDOM 29.63
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] -0.2829 -0.2829 0.5659
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.57 t_omega_torsion 3.63 t_angle_deg 0.97 t_bond_d 0.009 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 15.57 t_omega_torsion 3.63 t_angle_deg 0.97 t_bond_d 0.009 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 2460 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 25
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction