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Hexameric HIV-1 CA in complex with DDD00100439
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 53.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.61 α = 90 b = 90.61 β = 90 c = 56.8 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) 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 1.38 45.31 94.4 0.04 0.99 24 7.9 51571
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.38 1.4 63.2 0.64 0.58 1.6 2.4
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 1.38 45.31 49028 2541 94.35 0.17796 0.17659 0.184 0.20299 0.2113 RANDOM 29.869
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] 0.3 0.15 0.3 -0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.864 r_dihedral_angle_4_deg 26.807 r_long_range_B_other 14.771 r_long_range_B_refined 14.713 r_dihedral_angle_3_deg 14.009 r_mcangle_other 12.293 r_mcangle_it 12.292 r_mcbond_it 11.728 r_mcbond_other 11.725 r_scangle_other 10.847
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.864 r_dihedral_angle_4_deg 26.807 r_long_range_B_other 14.771 r_long_range_B_refined 14.713 r_dihedral_angle_3_deg 14.009 r_mcangle_other 12.293 r_mcangle_it 12.292 r_mcbond_it 11.728 r_mcbond_other 11.725 r_scangle_other 10.847 r_scbond_it 8.09 r_scbond_other 8.086 r_dihedral_angle_1_deg 5.968 r_angle_other_deg 3.711 r_angle_refined_deg 2.178 r_chiral_restr 0.138 r_bond_refined_d 0.028 r_gen_planes_other 0.022 r_gen_planes_refined 0.011 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 1696 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction xia2 data scaling MOLREP phasing