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HIV capsid hexamer with IP6 ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HGP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 277 PEG4K
Crystal Properties Matthews coefficient Solvent content 2.81 56.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.299 α = 90 b = 91.299 β = 90 c = 57.201 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 277 CCD OXFORD RUBY CCD 2017-01-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 1 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.9 79 91.5 0.084 10.8 4.6 21569
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 94.1 0.878 0.943 1.6 4.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5HGP 1.9 46.39 18790 967 91.61 0.18763 0.18573 0.22372 0.2384 RANDOM 36.23
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] -0.1 -0.05 -0.1 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.84 r_dihedral_angle_4_deg 22.485 r_dihedral_angle_3_deg 14.734 r_long_range_B_refined 8.081 r_long_range_B_other 8.031 r_scangle_other 6.521 r_dihedral_angle_1_deg 5.712 r_scbond_other 4.342 r_scbond_it 4.334 r_mcangle_it 4.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.84 r_dihedral_angle_4_deg 22.485 r_dihedral_angle_3_deg 14.734 r_long_range_B_refined 8.081 r_long_range_B_other 8.031 r_scangle_other 6.521 r_dihedral_angle_1_deg 5.712 r_scbond_other 4.342 r_scbond_it 4.334 r_mcangle_it 4.247 r_mcangle_other 4.245 r_mcbond_it 3.108 r_mcbond_other 3.107 r_angle_refined_deg 1.931 r_angle_other_deg 1.172 r_chiral_restr 0.48 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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 120 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing