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The Crystal Structure of integrase from Biortus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7UOQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 100mM sodium acetate at pH 5.3, 1.9M ammonium
Crystal Properties Matthews coefficient Solvent content 2.83 56.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.027 α = 90 b = 71.027 β = 90 c = 66.849 γ = 120
Symmetry Space Group P 31 2 1
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 EIGER X 9M 2022-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.953743 CLSI 08ID-1
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 1.55 45.306 100 0.08 19.1 15.1 28716
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 1.55 1.58 100 0.853 3.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.55 45.306 28716 1449 99.979 0.177 0.1761 0.1899 0.1986 0.204 25.388
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] 0.086 0.043 0.086 -0.278
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.672 r_dihedral_angle_3_deg 11.426 r_lrange_it 6.611 r_lrange_other 6.395 r_dihedral_angle_2_deg 6.15 r_dihedral_angle_1_deg 5.803 r_scangle_it 4.329 r_scangle_other 4.326 r_mcangle_it 3.057 r_mcangle_other 3.055
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.672 r_dihedral_angle_3_deg 11.426 r_lrange_it 6.611 r_lrange_other 6.395 r_dihedral_angle_2_deg 6.15 r_dihedral_angle_1_deg 5.803 r_scangle_it 4.329 r_scangle_other 4.326 r_mcangle_it 3.057 r_mcangle_other 3.055 r_scbond_it 2.766 r_scbond_other 2.764 r_mcbond_other 1.908 r_mcbond_it 1.907 r_angle_refined_deg 1.219 r_angle_other_deg 0.419 r_nbd_refined 0.235 r_nbd_other 0.209 r_nbtor_refined 0.18 r_symmetry_nbd_other 0.173 r_symmetry_nbd_refined 0.17 r_xyhbond_nbd_refined 0.165 r_symmetry_xyhbond_nbd_refined 0.159 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.057 r_symmetry_xyhbond_nbd_other 0.036 r_gen_planes_refined 0.007 r_bond_refined_d 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1179 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing