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Structure of HIV-1 CA 1/2-hexamer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H47 PDB entry 3H47
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8 293 0.1 M PCB buffer, pH 8 (sodium propionate, sodium cacodylate, Bis-Tris propane), 25% w/v PEG1500
Crystal Properties Matthews coefficient Solvent content 2.65 53.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.77 α = 70.65 b = 77.746 β = 70.7 c = 77.758 γ = 70.59
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2016-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.96 45 92.5 0.05 14.9 1.8 30532 99.19
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.96 3.01 86.03 0.351 0.9
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 PDB entry 3H47 2.96 45 29060 1471 92.49 0.21099 0.208 0.2051 0.26469 0.2526 RANDOM 103.954
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] 1.05 3.98 1.86 0.42 2.73 2.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.551 r_dihedral_angle_4_deg 21.917 r_long_range_B_other 20 r_long_range_B_refined 19.999 r_dihedral_angle_3_deg 17.085 r_mcangle_other 15.646 r_mcangle_it 15.645 r_scangle_other 14.775 r_mcbond_it 10.208 r_mcbond_other 10.201
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.551 r_dihedral_angle_4_deg 21.917 r_long_range_B_other 20 r_long_range_B_refined 19.999 r_dihedral_angle_3_deg 17.085 r_mcangle_other 15.646 r_mcangle_it 15.645 r_scangle_other 14.775 r_mcbond_it 10.208 r_mcbond_other 10.201 r_scbond_it 9.369 r_scbond_other 9.369 r_dihedral_angle_1_deg 7.332 r_angle_refined_deg 1.437 r_angle_other_deg 1.186 r_chiral_restr 0.058 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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 10061 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing Coot model building PHENIX refinement