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HIV-1 capsid C-terminal domain mutant (N183A) in complex with an inhibitor of particle assembly (CAI)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BUO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 4.2 298 32% PEG 4000, 100mM ammonium acetate pH4.2, 10mM MgCl2, EVAPORATION, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 1.9 35.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.838 α = 90 b = 42.838 β = 90 c = 90.495 γ = 90
Symmetry Space Group P 41 21 2
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 MARMOSAIC 225 mm CCD Dynamically bendable mirror 2007-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.044 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.6 38.7 99.4 0.079 0.079 25.6 13.9 11638 22.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.6 1.66 100 0.362 0.362 7.2 10.9 1140
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2BUO 1.6 38.72 11638 11086 551 99.22 0.20825 0.20636 0.2056 0.24545 0.2461 RANDOM 24.294
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] -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.649 r_dihedral_angle_4_deg 13.558 r_dihedral_angle_3_deg 11.926 r_dihedral_angle_1_deg 4.528 r_scangle_it 4.069 r_sphericity_free 3.972 r_scbond_it 2.791 r_sphericity_bonded 2.44 r_mcangle_it 1.846 r_rigid_bond_restr 1.705
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.649 r_dihedral_angle_4_deg 13.558 r_dihedral_angle_3_deg 11.926 r_dihedral_angle_1_deg 4.528 r_scangle_it 4.069 r_sphericity_free 3.972 r_scbond_it 2.791 r_sphericity_bonded 2.44 r_mcangle_it 1.846 r_rigid_bond_restr 1.705 r_angle_refined_deg 1.305 r_mcbond_it 1.184 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.254 r_nbd_refined 0.204 r_symmetry_hbond_refined 0.156 r_xyhbond_nbd_refined 0.119 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 733 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement RemDAq data collection DENZO data reduction SCALEPACK data scaling PHASER phasing