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Structure of the V11I/T58A/I124A mutant of the HIV-1 capsid protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XFX pdbid 4XFX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 PEG3350, NaI, Sodium cacodylate, Glycerol
Crystal Properties Matthews coefficient Solvent content 2.76 55.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.915 α = 90 b = 91.915 β = 90 c = 57.919 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 2016-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.000031 ALS 4.2.2
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 2.78 45.96 97.3 0.109 0.115 0.035 0.999 18 10.6 6969
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 2.78 2.93 97.3 1.05 1.106 0.345 0.754 9.9
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 pdbid 4XFX 2.78 45.96 6576 383 97.14 0.2156 0.2131 0.2265 0.26 0.2715 RANDOM 74.506
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] -0.39 -0.19 -0.39 1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.873 r_dihedral_angle_4_deg 18.695 r_dihedral_angle_3_deg 12.558 r_dihedral_angle_1_deg 5.467 r_angle_refined_deg 1.085 r_angle_other_deg 0.852 r_chiral_restr 0.054 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.873 r_dihedral_angle_4_deg 18.695 r_dihedral_angle_3_deg 12.558 r_dihedral_angle_1_deg 5.467 r_angle_refined_deg 1.085 r_angle_other_deg 0.852 r_chiral_restr 0.054 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1680 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 16
Software Software Software Name Purpose Aimless data scaling Blu-Ice data collection REFMAC refinement PDB_EXTRACT data extraction Aimless data reduction PHASER phasing