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X-ray structure of C-terminal domain of human T-cell lymphotropic virus type 1 (HTLV-1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LLJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 1.2 M ammonium tartrate dibasic, 150 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.53 51.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.408 α = 90 b = 97.408 β = 90 c = 97.408 γ = 90
Symmetry Space Group I 41 3 2
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 PILATUS3 S 6M 2018-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.8 39.77 100 0.077 0.095 0.055 0.993 7.4 5.4 41483
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 0.711 0.503 0.354 1.8
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 5LLJ 1.8 39.77 7615 418 99.987 0.181 0.1771 0.1802 0.2464 0.2514 51.44
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.714 r_dihedral_angle_4_deg 16.2 r_dihedral_angle_3_deg 16.105 r_lrange_it 10.227 r_lrange_other 9.957 r_scangle_it 9.367 r_scangle_other 9.354 r_mcangle_other 9.292 r_mcangle_it 9.27 r_scbond_it 8.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.714 r_dihedral_angle_4_deg 16.2 r_dihedral_angle_3_deg 16.105 r_lrange_it 10.227 r_lrange_other 9.957 r_scangle_it 9.367 r_scangle_other 9.354 r_mcangle_other 9.292 r_mcangle_it 9.27 r_scbond_it 8.062 r_dihedral_angle_1_deg 8.055 r_scbond_other 8.046 r_mcbond_it 8.039 r_mcbond_other 7.961 r_rigid_bond_restr 4.704 r_angle_refined_deg 1.861 r_angle_other_deg 1.47 r_symmetry_xyhbond_nbd_refined 0.544 r_symmetry_nbd_refined 0.33 r_xyhbond_nbd_refined 0.285 r_nbd_other 0.243 r_symmetry_nbd_other 0.206 r_nbd_refined 0.187 r_nbtor_refined 0.185 r_symmetry_xyhbond_nbd_other 0.13 r_symmetry_nbtor_other 0.097 r_chiral_restr 0.083 r_xyhbond_nbd_other 0.057 r_bond_other_d 0.015 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 425 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Coot model building PHASER phasing xia2 data reduction