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Hexameric HIV-1 CA in complex with DDD01829021
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 2.61 52.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.327 α = 90 b = 90.327 β = 90 c = 56.509 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 PILATUS 6M 2018-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
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 1.76 78.28 100 0.1 0.99 11.6 9.9 26170
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 1.76 1.81 100 0.81 0.46 2 9
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 1.76 50.23 24721 1264 99.05 0.20258 0.20035 0.2119 0.24552 0.255 RANDOM 27.91
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 0.03 0.07 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.52 r_dihedral_angle_4_deg 20.723 r_dihedral_angle_3_deg 14.944 r_long_range_B_refined 7.599 r_long_range_B_other 7.359 r_dihedral_angle_1_deg 5.543 r_scangle_other 5.337 r_mcangle_it 4.447 r_mcangle_other 4.446 r_scbond_it 3.673
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.52 r_dihedral_angle_4_deg 20.723 r_dihedral_angle_3_deg 14.944 r_long_range_B_refined 7.599 r_long_range_B_other 7.359 r_dihedral_angle_1_deg 5.543 r_scangle_other 5.337 r_mcangle_it 4.447 r_mcangle_other 4.446 r_scbond_it 3.673 r_scbond_other 3.671 r_mcbond_it 3.109 r_mcbond_other 3.091 r_angle_refined_deg 2.035 r_angle_other_deg 1.171 r_chiral_restr 0.129 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_bond_other_d 0.002 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 1666 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction xia2 data scaling MOLREP phasing