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Structure of the wild-type native full-length HIV-1 capsid protein in complex with ZW-1261
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XFZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 PEG 3350, NaI, Sodium Cacodylate, Glycerol
Crystal Properties Matthews coefficient Solvent content 2.61 52.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.9 α = 90 b = 90.9 β = 90 c = 56.14 γ = 120
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 16M 2020-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.7 45.71 97.9 0.108 0.118 0.996 13.62 7.208 7239 69.356
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.77 91.1 0.768 0.84 0.783 3.39 6.064
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 (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 THROUGHOUT 4XFZ 2.7 45.71 6881 356 97.85 0.1728 0.1686 0.1773 0.2533 0.2557 RANDOM 70.635
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] -0.36 -0.18 -0.36 1.16
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 93.971 r_dihedral_angle_2_deg 37.735 r_dihedral_angle_4_deg 22.429 r_sphericity_bonded 20.046 r_dihedral_angle_3_deg 17.883 r_dihedral_angle_1_deg 7.009 r_rigid_bond_restr 4.978 r_angle_refined_deg 1.893 r_angle_other_deg 1.371 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 93.971 r_dihedral_angle_2_deg 37.735 r_dihedral_angle_4_deg 22.429 r_sphericity_bonded 20.046 r_dihedral_angle_3_deg 17.883 r_dihedral_angle_1_deg 7.009 r_rigid_bond_restr 4.978 r_angle_refined_deg 1.893 r_angle_other_deg 1.371 r_chiral_restr 0.098 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1725 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction