☰ Navigation Tabs
CPSF6 defines a conserved capsid interface that modulates HIV-1 replication
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GON PDB ENTRY 2GON
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 17 DEGREES (SITTING DROPS).PROTEIN/ PEPTIDE SOLUTION (0.37 MM HIV-1 CAN AND 4 MM CPSF6313-327 IN 20 MM HEPES PH 7, 50 MM NACL, 1 MM DTT) WAS MIXED WITH RESERVOIR SOLUTION (20% W/V PEG 3350, 0.2 M POTASSIUM PHOSPHATE DIBASIC) IN A 1:1 MIX.
Crystal Properties Matthews coefficient Solvent content 2.14 42.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.56 α = 90 b = 46.36 β = 90 c = 80.82 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.8 20 95.8 0.044 14.5 3.4 13664 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2GON 1.813 36.251 2 13664 682 94.955 0.191 0.1867 0.1935 0.2729 0.2662 29.696
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] -0.196 0.08 0.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.554 r_sphericity_free 29.738 r_scbond_it 26.865 r_scangle_it 22.965 r_mcangle_it 19.95 r_dihedral_angle_4_deg 17.165 r_mcbond_it 17.136 r_dihedral_angle_3_deg 15.147 r_sphericity_bonded 13.93 r_mcbond_other 8.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.554 r_sphericity_free 29.738 r_scbond_it 26.865 r_scangle_it 22.965 r_mcangle_it 19.95 r_dihedral_angle_4_deg 17.165 r_mcbond_it 17.136 r_dihedral_angle_3_deg 15.147 r_sphericity_bonded 13.93 r_mcbond_other 8.093 r_dihedral_angle_1_deg 6.196 r_rigid_bond_restr 4.468 r_angle_refined_deg 1.656 r_angle_other_deg 0.847 r_nbd_other 0.262 r_nbd_refined 0.258 r_xyhbond_nbd_refined 0.24 r_nbtor_refined 0.173 r_chiral_restr 0.092 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbtor_other 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1178 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing