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PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00000422b
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Crystal Properties Matthews coefficient Solvent content 3.31 62.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.699 α = 90 b = 89.699 β = 90 c = 106.354 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 PILATUS 6M 2016-09-25 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
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 77.681 100 0.057 0.063 0.999 14.84 89573 -3 39.096
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 1.9 99.8 0.941 1.065 0.534 1.36
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 62.73 44949 1840 99.97 0.1921 0.1908 0.1985 0.2242 0.2295 RANDOM 38.144
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] 0.23 0.12 0.23 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.912 r_dihedral_angle_4_deg 20.142 r_dihedral_angle_3_deg 13.987 r_dihedral_angle_1_deg 6.532 r_mcangle_it 4.656 r_mcbond_other 3.349 r_mcbond_it 3.333 r_angle_refined_deg 1.697 r_angle_other_deg 1.439 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.912 r_dihedral_angle_4_deg 20.142 r_dihedral_angle_3_deg 13.987 r_dihedral_angle_1_deg 6.532 r_mcangle_it 4.656 r_mcbond_other 3.349 r_mcbond_it 3.333 r_angle_refined_deg 1.697 r_angle_other_deg 1.439 r_chiral_restr 0.094 r_bond_refined_d 0.028 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2317 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction PHASER phasing XDS data reduction