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N74D mutant of the HIV-1 capsid protein in complex with PF-3450074 (PF74)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XFX
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 2.56 51.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.358 α = 90 b = 90.358 β = 90 c = 55.695 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 PILATUS3 6M 2020-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.03317 APS 23-ID-D
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 2.65 45.38 98.5 0.092 0.101 0.041 0.998 11.2 5.5 7562
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 2.65 2.78 96.8 0.774 0.858 0.359 0.643 5.3
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 (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 4XFX 2.65 45.38 7190 366 98.63 0.1858 0.1828 0.1891 0.2421 0.2459 RANDOM 66.778
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] -0.31 -0.15 -0.31 0.99
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 63.808 r_sphericity_free 55.905 r_dihedral_angle_2_deg 37.574 r_dihedral_angle_3_deg 17.27 r_dihedral_angle_4_deg 17.093 r_dihedral_angle_1_deg 6.488 r_angle_refined_deg 1.96 r_angle_other_deg 1.138 r_chiral_restr 0.113 r_bond_refined_d 0.019
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 63.808 r_sphericity_free 55.905 r_dihedral_angle_2_deg 37.574 r_dihedral_angle_3_deg 17.27 r_dihedral_angle_4_deg 17.093 r_dihedral_angle_1_deg 6.488 r_angle_refined_deg 1.96 r_angle_other_deg 1.138 r_chiral_restr 0.113 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.006 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1725 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction