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The 1.1 Angstrom Structure of Catalytic Core Domain of FIV Integrase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F9K PDB ENTRY 3f9k
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 293 0.2M Trimethylamine N-oxide, 0.1M Tris pH 8.5, 20% PEG MME 2000, VAPOR DIFFUSION, temperature 293K 2 VAPOR DIFFUSION 5.5 293 0.2M Ammonium acetate, 0.1M Bis-Tris pH 5.5, 25% PEG 3350, VAPOR DIFFUSION, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.254 α = 90 b = 66.643 β = 103.43 c = 32.619 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 103 PIXEL DECTRIS PILATUS 6M mirrors 2013-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918409 BESSY 14.1
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 1.08 33.32 95.6 0.03 0.03 15.94 3.41 48083 47812 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.08 1.135 90.3 2.59
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3f9k 1.08 33.32 47812 45678 2405 95.48 0.14173 0.1399 0.1765 0.1741 RANDOM 17.061
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] 0.17 0.05 0.07 -0.21
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 43.451 r_dihedral_angle_2_deg 38.13 r_sphericity_bonded 17.379 r_dihedral_angle_3_deg 12.373 r_rigid_bond_restr 8.439 r_dihedral_angle_1_deg 5.609 r_angle_refined_deg 1.942 r_chiral_restr 0.121 r_bond_refined_d 0.02 r_gen_planes_refined 0.013
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 43.451 r_dihedral_angle_2_deg 38.13 r_sphericity_bonded 17.379 r_dihedral_angle_3_deg 12.373 r_rigid_bond_restr 8.439 r_dihedral_angle_1_deg 5.609 r_angle_refined_deg 1.942 r_chiral_restr 0.121 r_bond_refined_d 0.02 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_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_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1009 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms
Software Software Software Name Purpose MxCuBE data collection BALBES phasing REFMAC refinement XDS data reduction XDS data scaling