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Structure of HIV-1 integrase with native amino-terminal sequence
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K6Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 0.7 M NaH2PO4/1.0 M K2HPO4, 0.1M Na acetate
Crystal Properties Matthews coefficient Solvent content 3.96 68.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.919 α = 90 b = 102.919 β = 90 c = 279.203 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 100 PIXEL DECTRIS EIGER X 9M 2019-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.92013 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 96.65 100 0.11 0.99 8.1 26.6 59665 23.736314418
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 100 0.318 0.289 1.6 26.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 1K6Y 2.4 96.57 1.35116797642 59636 1169 99.9513952904 0.22525453281 0.224708598635 0.2242 0.252853510995 0.2508 Random selection 31.0729209873
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 f_dihedral_angle_d 15.8513640858 f_angle_d 0.588735515525 f_chiral_restr 0.0430533222458 f_bond_d 0.00351159142642 f_plane_restr 0.00340448790845
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5830 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 28
Software Software Software Name Purpose PHENIX refinement DIALS data reduction DIALS data scaling PHASER phasing