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Hexameric HIV-1 CA in complex with DDD01728501
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 2.66 53.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.76 α = 90 b = 90.76 β = 90 c = 57 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 2017-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 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 1.88 45.38 99.9 0.09 0.99 12.4 5.4 21682
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 1.88 1.91 98.1 1.03 0.52 1.6 4.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.88 45.38 20638 1040 98.95 0.18117 0.17946 0.21524 0.2103 RANDOM 30.399
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] 0.02 0.01 0.02 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.059 r_dihedral_angle_4_deg 22.513 r_dihedral_angle_3_deg 14.554 r_long_range_B_refined 7.708 r_long_range_B_other 7.706 r_scangle_other 6.13 r_dihedral_angle_1_deg 6.116 r_mcangle_it 4.329 r_mcangle_other 4.329 r_scbond_it 4.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.059 r_dihedral_angle_4_deg 22.513 r_dihedral_angle_3_deg 14.554 r_long_range_B_refined 7.708 r_long_range_B_other 7.706 r_scangle_other 6.13 r_dihedral_angle_1_deg 6.116 r_mcangle_it 4.329 r_mcangle_other 4.329 r_scbond_it 4.18 r_scbond_other 4.174 r_mcbond_it 3.039 r_mcbond_other 3.03 r_angle_refined_deg 1.979 r_angle_other_deg 1.136 r_chiral_restr 0.136 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 r_bond_other_d 0.006 r_gen_planes_other 0.002 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 1660 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction xia2 data scaling MOLREP phasing