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HIV-1 IN core domain in complex with 1-benzothiophen-6-amine 1,1-dioxide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3L3U PDB ENTRY 3l3u
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 295 1.6M AmSO4, 0.1M Na Citrate pH 5.6, 50mM CdCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.17 43.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.873 α = 90 b = 61.023 β = 90 c = 81.917 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 CCD MAR CCD 165 mm Mirror 2007-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-D 1.00 APS 14-BM-D
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 1.9 59.8 100 0.179 0.179 14.7 6.7 24337 24231 2 2
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 1.9 2 100 1.172 0.493 1.9 6.7
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 (All) 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 PDB ENTRY 3l3u 1.9 48.91 23055 22997 1236 99.75 0.2284 0.21517 0.21233 0.26914 0.2335 RANDOM 30.194
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] -0.77 2.63 -1.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.332 r_dihedral_angle_4_deg 19.99 r_dihedral_angle_3_deg 17.616 r_dihedral_angle_1_deg 7.032 r_angle_refined_deg 2.103 r_chiral_restr 0.137 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.332 r_dihedral_angle_4_deg 19.99 r_dihedral_angle_3_deg 17.616 r_dihedral_angle_1_deg 7.032 r_angle_refined_deg 2.103 r_chiral_restr 0.137 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 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_it r_mcbond_other r_mcangle_it r_scbond_it 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 2144 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 44
Software Software Software Name Purpose AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling