☰ Navigation Tabs
Two domain fragment of HIV-2 integrase in complex with LEDGF IBD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B4J PDB ENTRY 2B4J (chains A and C), 1K6Y (chain A residue 1-43) experimental model PDB 1K6Y PDB ENTRY 2B4J (chains A and C), 1K6Y (chain A residue 1-43)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 4.08 69.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 201.36 α = 90 b = 202.5 β = 90 c = 280.48 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 ADSC QUANTUM 315 2008-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9802 ESRF ID23-1
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 3.2 50 99.9 0.161 0.161 13 7.9 188554 188411 -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 3.2 3.37 100 100 0.562 0.562 3.9 8
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 PDB ENTRY 2B4J (chains A and C), 1K6Y (chain A residue 1-43) 3.2 34.99 178727 178727 9726 100 0.22538 0.22489 0.2249 0.23421 0.2343 THIN SHELLS 43.03
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 0.22 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.029 r_dihedral_angle_3_deg 17.683 r_dihedral_angle_4_deg 14.857 r_scangle_it 5.178 r_dihedral_angle_1_deg 4.867 r_scbond_it 2.782 r_mcangle_it 2.34 r_mcbond_it 1.153 r_angle_refined_deg 0.948 r_chiral_restr 0.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.029 r_dihedral_angle_3_deg 17.683 r_dihedral_angle_4_deg 14.857 r_scangle_it 5.178 r_dihedral_angle_1_deg 4.867 r_scbond_it 2.782 r_mcangle_it 2.34 r_mcbond_it 1.153 r_angle_refined_deg 0.948 r_chiral_restr 0.067 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 46692 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 48
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling