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Structure of PTP1b complexed with difluoromethylphosphonate inhibitor Compound 30
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 3.1 60.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.008 α = 90 b = 89.008 β = 90 c = 105.662 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 2021-06-11 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 1.898 77.083 89.1 0.999 14.6 9.7 34209 36.38
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 1.898 1.941 0.768
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 1.939 77.08 32605 1679 89.5 0.2037 0.202 0.1966 0.2356 0.2246 RANDOM 38.87
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] 2.2538 2.2538 -4.5075
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.69 t_omega_torsion 3.37 t_angle_deg 0.89 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 15.69 t_omega_torsion 3.37 t_angle_deg 0.89 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 2356 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 34
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction