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HIV-1 capsid C-terminal domain mutant (Y169A)
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 7.5 298 20% PEG 3350, 200mM sodium iodide, pH 7.5, EVAPORATION, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 1.93 36.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.67 α = 90 b = 75.66 β = 99.92 c = 32.87 γ = 90
Symmetry Space Group P 1 21 1
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 1.2 37.8 85.49 0.041 0.041 16.5 3.5 38077 10.3
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) 1.2 1.26 43.5 0.361 0.361 2.4 2.2 1705
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 1.2 27.27 36840 36840 1202 85.31 0.19249 0.19081 0.1927 0.2457 0.2439 RANDOM 14.464
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] -0.07 0.08 -0.11 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.154 r_dihedral_angle_1_deg 17.405 r_dihedral_angle_4_deg 12.733 r_dihedral_angle_3_deg 12.28 r_sphericity_free 11.545 r_scangle_it 6.847 r_sphericity_bonded 6.21 r_scbond_it 4.961 r_mcangle_it 3.707 r_rigid_bond_restr 2.956
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.154 r_dihedral_angle_1_deg 17.405 r_dihedral_angle_4_deg 12.733 r_dihedral_angle_3_deg 12.28 r_sphericity_free 11.545 r_scangle_it 6.847 r_sphericity_bonded 6.21 r_scbond_it 4.961 r_mcangle_it 3.707 r_rigid_bond_restr 2.956 r_mcbond_it 2.652 r_angle_refined_deg 2.201 r_chiral_restr 0.13 r_bond_refined_d 0.027 r_gen_planes_refined 0.014 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1317 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement RemDAq data collection XDS data reduction SCALA data scaling PHASER phasing