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PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with Z2856434762
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 3.3 62.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.618 α = 90 b = 89.618 β = 90 c = 106.406 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 2019-07-17 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 1.84 62.7 100 0.498 0.521 0.936 5.8 43422
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 1.84 1.87 99.95 4.008 4.21 0.264 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 1.84 62.7 40860 1677 98 0.1636 0.1624 0.1915 0.194 0.2187 RANDOM 37.483
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.328 r_dihedral_angle_4_deg 20.963 r_dihedral_angle_3_deg 15.178 r_dihedral_angle_1_deg 6.174 r_mcangle_it 4.216 r_mcbond_it 2.901 r_mcbond_other 2.889 r_angle_refined_deg 1.575 r_angle_other_deg 1.364 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.328 r_dihedral_angle_4_deg 20.963 r_dihedral_angle_3_deg 15.178 r_dihedral_angle_1_deg 6.174 r_mcangle_it 4.216 r_mcbond_it 2.901 r_mcbond_other 2.889 r_angle_refined_deg 1.575 r_angle_other_deg 1.364 r_chiral_restr 0.075 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2297 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2.multiplex data scaling DIALS data reduction DIMPLE phasing