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Hexameric HIV-1 (M-group) CA R120 mutant
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 6.5 293 9.5% PEG 3350 (v/v), 310 mM NaI, 100 mM Sodium Cacodylate. Crystals grew in 1 uL protein (3 mg/mL) + 1 uL crystallant. Cryoprotected in 20% (v/v) Glycerol.
Crystal Properties Matthews coefficient Solvent content 2.75 55.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.36 α = 90 b = 92.36 β = 90 c = 57.44 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 R 4M 2020-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 1.0332 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.304 79.98 98.4 0.071 0.997 10.76 3.9 12346
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.304 2.44 0.503 1
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 4XFX 2.304 46.656 12276 578 98.397 0.244 0.2423 0.2432 0.2775 0.2883 93.332
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] -5.699 -5.699 11.398
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.959 r_dihedral_angle_4_deg 24.062 r_dihedral_angle_3_deg 20.023 r_lrange_it 14.589 r_scangle_it 9.558 r_mcangle_it 8.903 r_scbond_it 6.813 r_mcbond_it 6.147 r_dihedral_angle_1_deg 5.43 r_angle_refined_deg 2.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.959 r_dihedral_angle_4_deg 24.062 r_dihedral_angle_3_deg 20.023 r_lrange_it 14.589 r_scangle_it 9.558 r_mcangle_it 8.903 r_scbond_it 6.813 r_mcbond_it 6.147 r_dihedral_angle_1_deg 5.43 r_angle_refined_deg 2.017 r_symmetry_xyhbond_nbd_refined 0.449 r_symmetry_nbd_refined 0.405 r_nbtor_refined 0.331 r_nbd_refined 0.301 r_xyhbond_nbd_refined 0.235 r_chiral_restr 0.141 r_gen_planes_refined 0.01 r_bond_refined_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1723 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing