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HIV-CA Disulfide linked Hexamer bound to Quinazolin-4-one Scaffold inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other HIV-1 Capsid hexamer
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 Morpheus D11
Crystal Properties Matthews coefficient Solvent content 2.72 54.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.174 α = 78.816 b = 91.326 β = 87.196 c = 117.518 γ = 60.116
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 PIXEL DECTRIS PILATUS 2M 2023-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU PhotonJet-S 1.5406
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.7 15.972 99 0.979 8.6 4.7 87509
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.75 99.7 0.522 4.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.7 15.972 87393 4195 98.82 0.222 0.2197 0.2232 0.2601 0.264 43.761
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] -0.103 0.234 -0.113 -0.149 -0.125 0.507
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.402 r_dihedral_angle_3_deg 16.451 r_dihedral_angle_6_deg 14.364 r_lrange_it 10.065 r_lrange_other 10.065 r_scangle_it 7.501 r_scangle_other 7.501 r_mcangle_it 7.202 r_mcangle_other 7.201 r_dihedral_angle_1_deg 6.799
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.402 r_dihedral_angle_3_deg 16.451 r_dihedral_angle_6_deg 14.364 r_lrange_it 10.065 r_lrange_other 10.065 r_scangle_it 7.501 r_scangle_other 7.501 r_mcangle_it 7.202 r_mcangle_other 7.201 r_dihedral_angle_1_deg 6.799 r_scbond_it 4.909 r_scbond_other 4.909 r_mcbond_it 4.702 r_mcbond_other 4.702 r_dihedral_angle_other_2_deg 2.969 r_angle_refined_deg 1.376 r_angle_other_deg 0.43 r_nbd_refined 0.228 r_nbd_other 0.218 r_symmetry_nbd_other 0.192 r_symmetry_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.183 r_symmetry_nbd_refined 0.147 r_xyhbond_nbd_refined 0.119 r_symmetry_xyhbond_nbd_other 0.089 r_symmetry_nbtor_other 0.077 r_ncsr_local_group_25 0.075 r_ncsr_local_group_26 0.073 r_chiral_restr 0.072 r_ncsr_local_group_28 0.07 r_ncsr_local_group_29 0.07 r_ncsr_local_group_7 0.069 r_ncsr_local_group_30 0.068 r_ncsr_local_group_9 0.066 r_ncsr_local_group_10 0.066 r_ncsr_local_group_27 0.066 r_ncsr_local_group_46 0.065 r_ncsr_local_group_40 0.064 r_ncsr_local_group_19 0.063 r_ncsr_local_group_34 0.063 r_ncsr_local_group_49 0.063 r_ncsr_local_group_11 0.062 r_ncsr_local_group_16 0.062 r_ncsr_local_group_37 0.062 r_ncsr_local_group_18 0.061 r_ncsr_local_group_21 0.061 r_ncsr_local_group_33 0.061 r_ncsr_local_group_35 0.061 r_ncsr_local_group_8 0.059 r_ncsr_local_group_20 0.059 r_ncsr_local_group_36 0.059 r_ncsr_local_group_43 0.059 r_ncsr_local_group_45 0.059 r_ncsr_local_group_48 0.059 r_ncsr_local_group_50 0.059 r_ncsr_local_group_5 0.058 r_ncsr_local_group_6 0.058 r_ncsr_local_group_42 0.058 r_ncsr_local_group_44 0.058 r_ncsr_local_group_47 0.058 r_ncsr_local_group_51 0.058 r_ncsr_local_group_38 0.057 r_ncsr_local_group_41 0.057 r_ncsr_local_group_2 0.056 r_ncsr_local_group_17 0.056 r_ncsr_local_group_24 0.054 r_ncsr_local_group_3 0.051 r_ncsr_local_group_55 0.051 r_ncsr_local_group_1 0.05 r_ncsr_local_group_23 0.05 r_ncsr_local_group_39 0.05 r_chiral_restr_other 0.049 r_ncsr_local_group_4 0.049 r_ncsr_local_group_61 0.048 r_ncsr_local_group_62 0.048 r_ncsr_local_group_22 0.047 r_ncsr_local_group_59 0.047 r_ncsr_local_group_12 0.046 r_ncsr_local_group_52 0.045 r_ncsr_local_group_57 0.045 r_ncsr_local_group_64 0.045 r_ncsr_local_group_63 0.044 r_ncsr_local_group_56 0.042 r_ncsr_local_group_60 0.041 r_ncsr_local_group_66 0.04 r_ncsr_local_group_53 0.039 r_ncsr_local_group_54 0.038 r_ncsr_local_group_65 0.038 r_ncsr_local_group_32 0.037 r_ncsr_local_group_31 0.035 r_ncsr_local_group_58 0.035 r_ncsr_local_group_13 0.032 r_ncsr_local_group_15 0.032 r_ncsr_local_group_14 0.028 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18592 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 684
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling PHASER phasing