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Hexameric HIV-1 CA in complex with DDD01044153
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HGM
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 2.63 53.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.472 α = 90 b = 90.472 β = 90 c = 56.688 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 CCD RIGAKU SATURN 944+ 2017-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
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 2.02 28.34 98.5 0.12 0.99 11 5.8 17180
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 2.02 2.13 89.7 0.47 0.79 3 4.3
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 2.02 28.34 16288 870 98.68 0.19133 0.18926 0.1949 0.23048 0.2414 RANDOM 25.968
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] 0.31 0.16 0.31 -1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.469 r_dihedral_angle_4_deg 21.848 r_dihedral_angle_3_deg 13.773 r_long_range_B_refined 6.201 r_long_range_B_other 6.201 r_dihedral_angle_1_deg 5.773 r_scangle_other 4.285 r_angle_other_deg 3.692 r_mcangle_it 3.605 r_mcangle_other 3.603
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.469 r_dihedral_angle_4_deg 21.848 r_dihedral_angle_3_deg 13.773 r_long_range_B_refined 6.201 r_long_range_B_other 6.201 r_dihedral_angle_1_deg 5.773 r_scangle_other 4.285 r_angle_other_deg 3.692 r_mcangle_it 3.605 r_mcangle_other 3.603 r_scbond_it 2.8 r_scbond_other 2.8 r_mcbond_it 2.473 r_mcbond_other 2.465 r_angle_refined_deg 1.77 r_chiral_restr 0.114 r_bond_refined_d 0.018 r_gen_planes_other 0.013 r_gen_planes_refined 0.009 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 1664 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing