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Structure of the native full-length 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 PEG3350, NaI, Sodium cacodylate
Crystal Properties Matthews coefficient Solvent content 2.73 54.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.181 α = 90 b = 92.181 β = 90 c = 56.976 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 CMOS RDI CMOS_8M 2014-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.00012 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.7 46.38 99.5 0.08 0.025 0.999 24.4 11.2 7709
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.83 96.5 1.682 0.535 0.714 1.8 10.7 975
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 FREE R-VALUE 4XFX 2.7 45 7347 354 99.57 0.2115 0.2102 0.2139 0.2406 0.238 RANDOM 88.088
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] -1.02 -0.51 -1.02 3.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.909 r_dihedral_angle_4_deg 25.668 r_dihedral_angle_3_deg 14.583 r_dihedral_angle_1_deg 5.726 r_mcangle_it 4.114 r_mcbond_it 2.603 r_mcbond_other 2.575 r_angle_refined_deg 1.45 r_angle_other_deg 0.917 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.909 r_dihedral_angle_4_deg 25.668 r_dihedral_angle_3_deg 14.583 r_dihedral_angle_1_deg 5.726 r_mcangle_it 4.114 r_mcbond_it 2.603 r_mcbond_other 2.575 r_angle_refined_deg 1.45 r_angle_other_deg 0.917 r_chiral_restr 0.07 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1663 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms 40
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction