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HIV-1 SF2 Nef in complex with the Fyn SH3 R96I mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D8D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293 0.10 M calcium acetate hydrate, 0.10 M sodium acetate buffer (pH 4.5), 10% w/v PEG 4000 2 VAPOR DIFFUSION, SITTING DROP 4.5 293 0.10 M calcium acetate hydrate, 0.10 M sodium acetate buffer (pH 4.5), 10% w/v PEG 4000 3 VAPOR DIFFUSION, SITTING DROP 4.5 293 0.10 M calcium acetate hydrate, 0.10 M sodium acetate buffer (pH 4.5), 10% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.32 46.97 2.32 46.97 2.32 46.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.11 α = 90 b = 122.11 β = 90 c = 145.89 γ = 120
Symmetry Space Group P 64 2 2
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 EIGER2 X 9M focusing bimorph mirrors in Kirkpatrick-Baez (KB) configuration 2020-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98011 SOLEIL PROXIMA 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 3.32 48.68 94.6 0.218 0.219 0.018 1 33.6 155.4 9209
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 3.324 3.46 42.1 9.136 9.163 0.71 0.486 1.1 165.4
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 4d8d 3.32 48.68 8283 923 92.24 0.28763 0.28616 0.2772 0.29953 0.2967 RANDOM 150.582
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] 0.98 0.49 0.98 -3.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.738 r_dihedral_angle_3_deg 19.364 r_dihedral_angle_4_deg 16.445 r_dihedral_angle_1_deg 6.355 r_angle_refined_deg 1.203 r_angle_other_deg 1.003 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.738 r_dihedral_angle_3_deg 19.364 r_dihedral_angle_4_deg 16.445 r_dihedral_angle_1_deg 6.355 r_angle_refined_deg 1.203 r_angle_other_deg 1.003 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2737 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction PDB_EXTRACT data extraction XSCALE data scaling MOLREP phasing