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CA-targeting nanobody is a tool for studying HIV-1 capsid lattice interactions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5O2U PDB entries 5O2U & 3H47 experimental model PDB 3H47 PDB entries 5O2U & 3H47
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 297 potassium nitrate, pH 6.9, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 3.77 67.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.548 α = 90 b = 140.378 β = 113.896 c = 125.186 γ = 90
Symmetry Space Group P 1 21 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-F 2018-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97910 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.45 50 96.2 0.11 0.134 0.077 6.6 2.8 39258 116.18
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.5 3.56 97.3 0.822 1.005 0.571 0.548 2.8
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 PDB entries 5O2U & 3H47 3.45 46.88 1.35 39215 1997 91.94 0.2147 0.2123 0.2114 0.2575 0.2574 RANDOM 168.99
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 4.6246 f_angle_d 1.3996 f_chiral_restr 0.0766 f_plane_restr 0.0085 f_bond_d 0.0071
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15089 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement DENZO data reduction HKL-2000 data scaling PDB_EXTRACT data extraction PHASER phasing