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Hexameric HIV-1 CA in complex with DDD00100555
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HGM Hexameric HIV-1 CA in complex with dATP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 0.1M Tris buffer, pH 8.0 to 9.0, 10-15% PEG550MME, 0.15M KSCN
Crystal Properties Matthews coefficient Solvent content 2.64 53.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.65 α = 90 b = 90.65 β = 90 c = 56.68 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 EIGER2 XE 16M 2016-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.67 56.68 100 0.07 19.4 10 30894
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.67 1.7 100 1.4 1.8 9.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.67 56.68 29356 1538 100 0.177 0.175 0.1854 0.21 0.2135 RANDOM 31.18
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] -0.07 -0.04 -0.07 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.277 r_dihedral_angle_4_deg 22.722 r_dihedral_angle_3_deg 14.223 r_long_range_B_refined 7.658 r_long_range_B_other 7.542 r_scangle_other 6.229 r_dihedral_angle_1_deg 6.065 r_mcangle_it 4.361 r_mcangle_other 4.361 r_scbond_it 4.349
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.277 r_dihedral_angle_4_deg 22.722 r_dihedral_angle_3_deg 14.223 r_long_range_B_refined 7.658 r_long_range_B_other 7.542 r_scangle_other 6.229 r_dihedral_angle_1_deg 6.065 r_mcangle_it 4.361 r_mcangle_other 4.361 r_scbond_it 4.349 r_scbond_other 4.347 r_angle_other_deg 3.696 r_mcbond_it 3.224 r_mcbond_other 3.222 r_angle_refined_deg 2.278 r_chiral_restr 0.146 r_bond_refined_d 0.027 r_gen_planes_other 0.021 r_gen_planes_refined 0.013 r_bond_other_d 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1670 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data reduction xia2 data scaling MOLREP phasing