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Crystal structure of a PP2A B56y/HTLV-1 integrase complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JAK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 293.15 0.1 M Na/KPO4 pH 6.2, 20-% 1,2-propanediol, 10% glycerol
Crystal Properties Matthews coefficient Solvent content 2.55 51.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.77 α = 90 b = 58.77 β = 90 c = 321.15 γ = 90
Symmetry Space Group P 43 21 2
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 PILATUS3 6M 2017-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9192 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 3.16 80.29 96.7 0.167 0.167 0.918 3.3 1.4 10041
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.16 3.38 94.4 0.489 0.589 1.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2JAK 3.164 80.29 10041 537 95.912 0.231 0.227 0.2214 0.2941 0.2983 57.582
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] 0.25 0.25 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.698 r_dihedral_angle_4_deg 25.598 r_dihedral_angle_3_deg 22.322 r_lrange_it 13.179 r_scangle_it 9.878 r_dihedral_angle_1_deg 9.354 r_mcangle_it 8.127 r_scbond_it 6.471 r_mcbond_it 5.316 r_angle_refined_deg 1.655
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.698 r_dihedral_angle_4_deg 25.598 r_dihedral_angle_3_deg 22.322 r_lrange_it 13.179 r_scangle_it 9.878 r_dihedral_angle_1_deg 9.354 r_mcangle_it 8.127 r_scbond_it 6.471 r_mcbond_it 5.316 r_angle_refined_deg 1.655 r_nbtor_refined 0.33 r_symmetry_nbd_refined 0.304 r_nbd_refined 0.282 r_xyhbond_nbd_refined 0.16 r_symmetry_xyhbond_nbd_refined 0.146 r_chiral_restr 0.14 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2674 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Coot model building xia2 data reduction PHASER phasing