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Structure of the HTLV-2 integrase catalytic core domain in complex with magnesium (dimeric form)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 100 mM Tris pH 8.5, 14% PEG 8000, 250 mM magnesium chloride
Crystal Properties Matthews coefficient Solvent content 3.45 69.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 185.315 α = 90 b = 89.175 β = 102.485 c = 65.53 γ = 90
Symmetry Space Group C 1 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 291 PIXEL DECTRIS PILATUS3 S 6M 2017-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.45 58.611 100 0.242 0.342 0.146 0.923 3 3.9 38400
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.55 100 0.383 3.9
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6QBV 2.45 58.611 38400 1876 99.914 0.235 0.2326 0.2364 0.2725 0.278 0.05 69.472
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] 5.006 2.061 -4.528 -1.267
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.83 r_dihedral_angle_4_deg 18.495 r_dihedral_angle_3_deg 17.359 r_lrange_it 13.143 r_scangle_it 11.427 r_mcangle_it 9.157 r_scbond_it 8.832 r_dihedral_angle_1_deg 7.074 r_mcbond_it 6.812 r_angle_refined_deg 1.624
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.83 r_dihedral_angle_4_deg 18.495 r_dihedral_angle_3_deg 17.359 r_lrange_it 13.143 r_scangle_it 11.427 r_mcangle_it 9.157 r_scbond_it 8.832 r_dihedral_angle_1_deg 7.074 r_mcbond_it 6.812 r_angle_refined_deg 1.624 r_nbtor_refined 0.312 r_nbd_refined 0.224 r_symmetry_xyhbond_nbd_refined 0.224 r_symmetry_nbd_refined 0.182 r_xyhbond_nbd_refined 0.175 r_chiral_restr 0.127 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4640 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement Coot model building xia2 data reduction PHASER phasing