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PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00000646b
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 3.38 63.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.413 α = 90 b = 90.413 β = 90 c = 107.001 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 1.9 63.189 99.7 0.063 0.071 0.999 14.09 76758 -3 44.393
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 1.9 2.02 99.3 1.351 1.509 0.541 1.07
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 1.9 63.19 37872 1548 97.86 0.198 0.1967 0.2185 0.2307 0.2539 RANDOM 45.513
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] 0.43 0.22 0.43 -1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.354 r_dihedral_angle_4_deg 18.71 r_dihedral_angle_3_deg 16.067 r_dihedral_angle_1_deg 6.77 r_mcangle_it 4.9 r_mcbond_it 4.36 r_mcbond_other 4.333 r_angle_refined_deg 1.614 r_angle_other_deg 1.346 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.354 r_dihedral_angle_4_deg 18.71 r_dihedral_angle_3_deg 16.067 r_dihedral_angle_1_deg 6.77 r_mcangle_it 4.9 r_mcbond_it 4.36 r_mcbond_other 4.333 r_angle_refined_deg 1.614 r_angle_other_deg 1.346 r_chiral_restr 0.089 r_bond_refined_d 0.026 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2317 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction PHASER phasing XDS data reduction