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PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with XST00000217b
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 62.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.465 α = 90 b = 89.465 β = 90 c = 106.381 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 2019-07-27 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 2.01 53.19 94.87 0.133 0.144 0.995 7.4 31617
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 2.01 2.04 99.22 1.58 1.721 0.255 0.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.01 44.77 30150 1248 94.27 0.1713 0.1695 0.2169 0.2547 RANDOM 46.699
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 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.405 r_dihedral_angle_4_deg 23.538 r_dihedral_angle_3_deg 15.857 r_dihedral_angle_1_deg 6.469 r_mcangle_it 4.661 r_mcbond_it 3.205 r_mcbond_other 3.169 r_angle_refined_deg 1.461 r_angle_other_deg 1.278 r_chiral_restr 0.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.405 r_dihedral_angle_4_deg 23.538 r_dihedral_angle_3_deg 15.857 r_dihedral_angle_1_deg 6.469 r_mcangle_it 4.661 r_mcbond_it 3.205 r_mcbond_other 3.169 r_angle_refined_deg 1.461 r_angle_other_deg 1.278 r_chiral_restr 0.069 r_bond_refined_d 0.023 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2297 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2.multiplex data scaling DIALS data reduction DIMPLE phasing