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Hexameric HIV-1 CA in complex with DDD01728505
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 2.77 55.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.345 α = 90 b = 90.345 β = 90 c = 56.581 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+ 2017-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.2 45.17 100 0.29 5.5 7.1 13511
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 2.2 2.32 100 1.33 0.58 1.9 7.1
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 2.2 35.33 12859 641 99.8 0.224 0.221 0.226 0.288 0.2898 RANDOM 30.49
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] 0.23 0.12 0.23 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.686 r_dihedral_angle_4_deg 22.153 r_dihedral_angle_1_deg 18.25 r_dihedral_angle_3_deg 15.307 r_long_range_B_refined 6.265 r_long_range_B_other 6.171 r_scangle_other 4.157 r_mcangle_it 3.689 r_mcangle_other 3.687 r_scbond_it 2.621
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.686 r_dihedral_angle_4_deg 22.153 r_dihedral_angle_1_deg 18.25 r_dihedral_angle_3_deg 15.307 r_long_range_B_refined 6.265 r_long_range_B_other 6.171 r_scangle_other 4.157 r_mcangle_it 3.689 r_mcangle_other 3.687 r_scbond_it 2.621 r_scbond_other 2.619 r_mcbond_it 2.362 r_mcbond_other 2.355 r_angle_refined_deg 1.464 r_angle_other_deg 1.355 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1683 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing