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HIV capsid hexamer with IP5 ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ES8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 270 PEG 6K, 1M NaCl
Crystal Properties Matthews coefficient Solvent content 2.94 58.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.663 α = 90 b = 90.663 β = 90 c = 56.997 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 OXFORD SAPPHIRE CCD 2019-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.978 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 1.913 78.52 99.3 0.056 0.998 17.7 6.5 20758
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 1.93 1.98 90 0.62 0.883 2.6 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6ES8 1.92 29.69 19575 972 98.96 0.19308 0.19111 0.203 0.23426 0.2432 RANDOM 35.456
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] -0.04 -0.02 -0.04 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.226 r_dihedral_angle_1_deg 23.408 r_dihedral_angle_4_deg 23.091 r_dihedral_angle_3_deg 15.556 r_long_range_B_refined 7.24 r_long_range_B_other 7.179 r_scangle_other 5.533 r_mcangle_it 4.393 r_mcangle_other 4.392 r_scbond_other 3.794
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.226 r_dihedral_angle_1_deg 23.408 r_dihedral_angle_4_deg 23.091 r_dihedral_angle_3_deg 15.556 r_long_range_B_refined 7.24 r_long_range_B_other 7.179 r_scangle_other 5.533 r_mcangle_it 4.393 r_mcangle_other 4.392 r_scbond_other 3.794 r_scbond_it 3.788 r_mcbond_it 3.275 r_mcbond_other 3.27 r_angle_refined_deg 1.652 r_angle_other_deg 1.409 r_chiral_restr 0.092 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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 1580 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing