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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 295 100 mM Bis-Tris propane, pH 6.8, 15% PEG3350, 200 mM sodium
Crystal Properties Matthews coefficient Solvent content 4.23 70.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.95 α = 90 b = 137.85 β = 90 c = 313.832 γ = 90
Symmetry Space Group I 2 2 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 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 1.0711 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 3.5 50 95.9 0.182 0.216 0.114 5 3.3 33153
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 98.7 1.179 1.405 0.748 0.38 3.3
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 PDB entries 5O2U & 3H47 3.511 49.581 33142 1668 94.389 0.246 0.2449 0.245 0.2699 0.2695 180.204
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] 0.4 2.014 -2.414
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.926 r_lrange_it 19.575 r_dihedral_angle_4_deg 15.919 r_dihedral_angle_3_deg 14.578 r_mcangle_it 11.904 r_scangle_it 11.721 r_scbond_it 7.575 r_mcbond_it 7.218 r_dihedral_angle_1_deg 5.008 r_angle_refined_deg 1.602
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.926 r_lrange_it 19.575 r_dihedral_angle_4_deg 15.919 r_dihedral_angle_3_deg 14.578 r_mcangle_it 11.904 r_scangle_it 11.721 r_scbond_it 7.575 r_mcbond_it 7.218 r_dihedral_angle_1_deg 5.008 r_angle_refined_deg 1.602 r_symmetry_xyhbond_nbd_refined 0.39 r_nbtor_refined 0.321 r_symmetry_nbd_refined 0.314 r_nbd_refined 0.232 r_ncsr_local_group_5 0.231 r_ncsr_local_group_6 0.22 r_ncsr_local_group_8 0.196 r_ncsr_local_group_4 0.194 r_xyhbond_nbd_refined 0.19 r_ncsr_local_group_9 0.184 r_ncsr_local_group_7 0.18 r_ncsr_local_group_1 0.158 r_ncsr_local_group_2 0.158 r_ncsr_local_group_3 0.152 r_ext_dist_refined_d 0.094 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11458 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction HKL-2000 data scaling PHASER phasing