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PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with Z2856434917
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 62.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.589 α = 90 b = 89.589 β = 90 c = 106.334 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 1.79 53.17 100 0.128 0.135 0.967 8.3 47018
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 1.79 1.82 100 2.831 2.996 0.335 0.4
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 1.79 44.83 42950 1763 95.11 0.163 0.1619 0.2021 0.1918 0.2254 RANDOM 40.476
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 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.761 r_dihedral_angle_4_deg 19.445 r_dihedral_angle_3_deg 16.597 r_dihedral_angle_1_deg 6.363 r_mcangle_it 4.593 r_mcbond_it 3.495 r_mcbond_other 3.469 r_angle_refined_deg 1.593 r_angle_other_deg 1.375 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.761 r_dihedral_angle_4_deg 19.445 r_dihedral_angle_3_deg 16.597 r_dihedral_angle_1_deg 6.363 r_mcangle_it 4.593 r_mcbond_it 3.495 r_mcbond_other 3.469 r_angle_refined_deg 1.593 r_angle_other_deg 1.375 r_chiral_restr 0.083 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2297 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2.multiplex data scaling DIALS data reduction DIMPLE phasing