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Hexameric HIV-1 CA in complex with DDD00024969
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HGM Hexameric HIV-1 CA in complex with dATP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 0.1M Tris buffer, pH 8.0 to 9.0, 10-15% PEG550MME, 0.15M KSCN
Crystal Properties Matthews coefficient Solvent content 2.75 55.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.805 α = 90 b = 91.805 β = 90 c = 57.59 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 100 PIXEL DECTRIS EIGER2 XE 16M 2016-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.69 28.8 99.8 0.059 0.99 20.4 9.2 31130
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.69 1.73 98.6 0.62 0.78 2.6 6.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.69 28.8 29474 1562 99.49 0.17529 0.17315 0.21618 0.2214 RANDOM 28.33
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] 0.27 0.13 0.27 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.72 r_dihedral_angle_4_deg 22.38 r_dihedral_angle_3_deg 14.332 r_long_range_B_refined 7.711 r_long_range_B_other 7.526 r_dihedral_angle_1_deg 6.02 r_scangle_other 5.81 r_mcangle_other 4.284 r_mcangle_it 4.279 r_scbond_it 3.986
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.72 r_dihedral_angle_4_deg 22.38 r_dihedral_angle_3_deg 14.332 r_long_range_B_refined 7.711 r_long_range_B_other 7.526 r_dihedral_angle_1_deg 6.02 r_scangle_other 5.81 r_mcangle_other 4.284 r_mcangle_it 4.279 r_scbond_it 3.986 r_scbond_other 3.984 r_angle_other_deg 3.794 r_mcbond_it 2.999 r_mcbond_other 2.973 r_angle_refined_deg 2.12 r_chiral_restr 0.147 r_bond_refined_d 0.027 r_gen_planes_other 0.02 r_gen_planes_refined 0.012 r_bond_other_d 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 1664 Nucleic Acid Atoms Solvent Atoms 295 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling MOLREP phasing