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PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with Z2856434906
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M HEPES, 0.3 M magnesium acetate, 13.5% PEG 8000, 2% ethanol, and 1 mM BME
Crystal Properties Matthews coefficient Solvent content 3.29 62.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.527 α = 90 b = 89.527 β = 90 c = 106.242 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 277 PIXEL DECTRIS PILATUS 6M 2019-07-22 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96874 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.83 62.63 99.99 0.151 0.162 0.987 8.6 43932
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 1.86 100 2.976 3.192 0.299 0.5
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 1.83 62.63 42135 1727 99.9 0.177 0.175 0.278 0.214 0.2894 RANDOM 41.83
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] -0.01 -0.01 -0.01 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.416 r_dihedral_angle_4_deg 18.704 r_dihedral_angle_3_deg 16.424 r_dihedral_angle_1_deg 6.132 r_mcangle_it 4.067 r_mcbond_other 3.533 r_mcbond_it 3.531 r_angle_refined_deg 1.512 r_angle_other_deg 1.318 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.416 r_dihedral_angle_4_deg 18.704 r_dihedral_angle_3_deg 16.424 r_dihedral_angle_1_deg 6.132 r_mcangle_it 4.067 r_mcbond_other 3.533 r_mcbond_it 3.531 r_angle_refined_deg 1.512 r_angle_other_deg 1.318 r_chiral_restr 0.075 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 2427 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2.multiplex data scaling DIALS data reduction DIMPLE phasing