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Crystal Structure of Catalytic Core domain of FIV Integrase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F9K 3f9ka
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 30% PEG 4000, 200 mM MgCl2, 100 mM TrisHCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.3 46.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.924 α = 90 b = 52.924 β = 90 c = 193.569 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS HTC 2014-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-X 1.54178
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 1.84 45.83 90.6 0.09952 29.66 15.2 13341 22.81
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.844 1.91 88.21 0.3539 6.74 13.8
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 3f9ka 1.84 45.83 12657 684 90.45 0.17375 0.17131 0.1828 0.22155 0.2266 RANDOM 26.893
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] 0.18 0.09 0.18 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.62 r_dihedral_angle_4_deg 20.564 r_dihedral_angle_3_deg 15.992 r_long_range_B_refined 15.919 r_long_range_B_other 14.773 r_scangle_other 6.093 r_dihedral_angle_1_deg 5.964 r_scbond_it 3.945 r_scbond_other 3.942 r_mcangle_it 3.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.62 r_dihedral_angle_4_deg 20.564 r_dihedral_angle_3_deg 15.992 r_long_range_B_refined 15.919 r_long_range_B_other 14.773 r_scangle_other 6.093 r_dihedral_angle_1_deg 5.964 r_scbond_it 3.945 r_scbond_other 3.942 r_mcangle_it 3.198 r_mcangle_other 3.196 r_mcbond_other 2.29 r_mcbond_it 2.288 r_angle_refined_deg 1.812 r_angle_other_deg 0.928 r_chiral_restr 0.121 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 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 1188 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms
Software Software Software Name Purpose HKL-3000 data scaling REFMAC refinement